Multiple platform build/check report for BioC 3.11 - CHECK report for pcaExplorer on tokay2

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

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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
###
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* 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.

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###
### 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


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


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

name	user	system	elapsed
correlatePCs	2.20	0.20	2.41
distro_expr	2.27	0.01	2.28
geneprofiler	1.61	0.15	1.75
genespca	2.90	0.01	2.92
get_annotation	3.64	0.59	4.24
get_annotation_orgdb	2.50	0.07	2.56
hi_loadings	2.14	0.08	2.22
limmaquickpca2go	2.86	0.10	2.97
makeExampleDESeqDataSet_multifac	0.48	0.00	0.49
pair_corr	2.71	0.07	2.79
pca2go	2.23	0.01	2.25
pcaExplorer	2.50	0.05	2.55
pcaplot	2.20	0.05	2.25
pcaplot3d	1.71	0.01	3.50
pcascree	2.70	0.02	2.72
plotPCcorrs	2.88	0.04	2.92
topGOtable	4.18	0.10	4.28

name	user	system	elapsed
correlatePCs	3.03	0.03	3.06
distro_expr	2.00	0.02	2.02
geneprofiler	1.37	0.00	1.37
genespca	2.28	0.02	2.29
get_annotation	3.74	0.03	3.77
get_annotation_orgdb	1.88	0.09	1.97
hi_loadings	2.21	0.00	2.20
limmaquickpca2go	1.82	0.05	1.86
makeExampleDESeqDataSet_multifac	0.29	0.00	0.29
pair_corr	1.85	0.03	1.88
pca2go	1.92	0.08	2.00
pcaExplorer	1.98	0.06	2.05
pcaplot	2.19	0.02	2.20
pcaplot3d	1.53	0.01	1.55
pcascree	1.83	0.00	1.82
plotPCcorrs	1.80	0.02	1.82
topGOtable	1.85	0.02	1.86

CHECK report for pcaExplorer on tokay2

Summary

Command output

Installation output

Tests output

Example timings