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CHECK report for pcaExplorer on tokay2

This page was generated on 2020-10-17 11:57:22 -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: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pcaExplorer_2.14.2.tar.gz
StartedAt: 2020-10-17 06:47:01 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:58:48 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 707.0 seconds
RetCode: 0
Status:  OK  
CheckDir: pcaExplorer.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pcaExplorer_2.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/pcaExplorer.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/pcaExplorer.Rcheck/00check.log'
for details.



Installation output

pcaExplorer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/pcaExplorer_2.14.2.tar.gz && rm -rf pcaExplorer.buildbin-libdir && mkdir pcaExplorer.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pcaExplorer.buildbin-libdir pcaExplorer_2.14.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL pcaExplorer_2.14.2.zip && rm pcaExplorer_2.14.2.tar.gz pcaExplorer_2.14.2.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 22.3M  100 22.3M    0     0  86.4M      0 --:--:-- --:--:-- --:--:-- 88.8M

install for i386

* installing *source* package 'pcaExplorer' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pcaExplorer'
    finding HTML links ... done
    correlatePCs                            html  
    distro_expr                             html  
    finding level-2 HTML links ... done

    geneprofiler                            html  
    genespca                                html  
    get_annotation                          html  
    get_annotation_orgdb                    html  
    hi_loadings                             html  
    limmaquickpca2go                        html  
    makeExampleDESeqDataSet_multifac        html  
    pair_corr                               html  
    pca2go                                  html  
    pcaExplorer-pkg                         html  
    pcaExplorer                             html  
    pcaplot                                 html  
    pcaplot3d                               html  
    pcascree                                html  
    plotPCcorrs                             html  
    topGOtable                              html  
** 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

install for x64

* installing *source* package 'pcaExplorer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pcaExplorer' as pcaExplorer_2.14.2.zip
* DONE (pcaExplorer)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'pcaExplorer' successfully unpacked and MD5 sums checked

Tests output

pcaExplorer.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  62.67    2.20   68.42 

pcaExplorer.Rcheck/tests_x64/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-w64-mingw32/x64 (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 
  69.90    1.25   74.37 

Example timings

pcaExplorer.Rcheck/examples_i386/pcaExplorer-Ex.timings

nameusersystemelapsed
correlatePCs2.200.202.41
distro_expr2.270.012.28
geneprofiler1.610.151.75
genespca2.900.012.92
get_annotation3.640.594.24
get_annotation_orgdb2.500.072.56
hi_loadings2.140.082.22
limmaquickpca2go2.860.102.97
makeExampleDESeqDataSet_multifac0.480.000.49
pair_corr2.710.072.79
pca2go2.230.012.25
pcaExplorer2.500.052.55
pcaplot2.200.052.25
pcaplot3d1.710.013.50
pcascree2.700.022.72
plotPCcorrs2.880.042.92
topGOtable4.180.104.28

pcaExplorer.Rcheck/examples_x64/pcaExplorer-Ex.timings

nameusersystemelapsed
correlatePCs3.030.033.06
distro_expr2.000.022.02
geneprofiler1.370.001.37
genespca2.280.022.29
get_annotation3.740.033.77
get_annotation_orgdb1.880.091.97
hi_loadings2.210.002.20
limmaquickpca2go1.820.051.86
makeExampleDESeqDataSet_multifac0.290.000.29
pair_corr1.850.031.88
pca2go1.920.082.00
pcaExplorer1.980.062.05
pcaplot2.190.022.20
pcaplot3d1.530.011.55
pcascree1.830.001.82
plotPCcorrs1.800.021.82
topGOtable1.850.021.86