Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-20 15:05:22 -0400 (Mon, 20 Sep 2021).

CHECK results for pcaExplorer on tokay2

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? here 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 1356/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pcaExplorer 2.18.0  (landing page)
Federico Marini
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/pcaExplorer
git_branch: RELEASE_3_13
git_last_commit: 724482a
git_last_commit_date: 2021-05-19 12:19:46 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: pcaExplorer
Version: 2.18.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pcaExplorer_2.18.0.tar.gz
StartedAt: 2021-09-20 02:36:37 -0400 (Mon, 20 Sep 2021)
EndedAt: 2021-09-20 02:46:35 -0400 (Mon, 20 Sep 2021)
EllapsedTime: 598.5 seconds
RetCode: 0
Status:   OK  
CheckDir: pcaExplorer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pcaExplorer_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/pcaExplorer.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '2.18.0'
* 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 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-3.13-bioc/meat/pcaExplorer.Rcheck/00check.log'
for details.



Installation output

pcaExplorer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/pcaExplorer_2.18.0.tar.gz && rm -rf pcaExplorer.buildbin-libdir && mkdir pcaExplorer.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pcaExplorer.buildbin-libdir pcaExplorer_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL pcaExplorer_2.18.0.zip && rm pcaExplorer_2.18.0.tar.gz pcaExplorer_2.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  7 22.3M    7 1821k    0     0  2601k      0  0:00:08 --:--:--  0:00:08 2602k
 26 22.3M   26 6042k    0     0  3534k      0  0:00:06  0:00:01  0:00:05 3533k
 48 22.3M   48 10.7M    0     0  4104k      0  0:00:05  0:00:02  0:00:03 4104k
 74 22.3M   74 16.7M    0     0  4638k      0  0:00:04  0:00:03  0:00:01 4638k
100 22.3M  100 22.3M    0     0  5032k      0  0:00:04  0:00:04 --:--:-- 5033k

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_2.18.0.zip
* DONE (pcaExplorer)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'pcaExplorer' successfully unpacked and MD5 sums checked

Tests output

pcaExplorer.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 v2.18.0

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 1 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  70.54    2.89   73.43 

pcaExplorer.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 v2.18.0

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 1 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  72.48    1.65   74.12 

Example timings

pcaExplorer.Rcheck/examples_i386/pcaExplorer-Ex.timings

nameusersystemelapsed
correlatePCs3.450.503.95
distro_expr3.580.103.67
geneprofiler3.080.053.12
genespca3.340.013.36
get_annotation2.740.363.09
get_annotation_orgdb2.560.032.60
hi_loadings2.580.002.58
limmaquickpca2go2.360.052.40
makeExampleDESeqDataSet_multifac0.670.000.67
pair_corr2.520.062.58
pca2go3.010.053.06
pcaExplorer2.250.062.31
pcaplot3.920.003.92
pcaplot3d2.560.023.27
pcascree3.030.003.03
plotPCcorrs2.670.002.67
topGOtable2.380.062.44

pcaExplorer.Rcheck/examples_x64/pcaExplorer-Ex.timings

nameusersystemelapsed
correlatePCs3.720.153.87
distro_expr3.240.053.28
geneprofiler2.880.002.87
genespca3.680.013.71
get_annotation3.660.103.76
get_annotation_orgdb3.340.123.47
hi_loadings3.230.143.37
limmaquickpca2go2.020.112.13
makeExampleDESeqDataSet_multifac0.660.000.65
pair_corr2.040.052.10
pca2go2.280.032.31
pcaExplorer2.720.092.81
pcaplot3.960.023.97
pcaplot3d4.510.024.53
pcascree3.430.003.44
plotPCcorrs3.110.013.12
topGOtable3.520.053.56