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CHECK report for BiocPkgTools on tokay2

This page was generated on 2020-10-17 11:56:09 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BiocPkgTools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 163/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.6.0
Sean Davis
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/BiocPkgTools
Branch: RELEASE_3_11
Last Commit: 60dc59e
Last Changed Date: 2020-04-27 15:19:21 -0400 (Mon, 27 Apr 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: BiocPkgTools
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocPkgTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BiocPkgTools_1.6.0.tar.gz
StartedAt: 2020-10-17 01:57:13 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:05:12 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 479.6 seconds
RetCode: 0
Status:  OK  
CheckDir: BiocPkgTools.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:BiocPkgTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BiocPkgTools_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/BiocPkgTools.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 'BiocPkgTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiocPkgTools' version '1.6.0'
* 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 'BiocPkgTools' 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 ... NOTE
Namespace in Imports field not imported from: 'rappdirs'
  All declared Imports should be used.
Unexported object imported by a ':::' call: 'BiocManager:::.repositories'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
get_bioc_data               35.17   0.17   35.40
biocDownloadStats           26.83   0.25   27.50
firstInBioc                 25.87   0.22   26.14
buildPkgDependencyDataFrame 17.36   0.26   17.64
pkgDepMetrics               14.38   0.44   14.98
pkgCombDependencyGain       12.75   0.52   13.42
biocPkgList                  8.46   0.13    8.87
buildPkgDependencyIgraph     7.72   0.05    7.78
getBiocVignette              7.35   0.14    7.53
inducedSubgraphByPkgs        6.89   0.09    7.05
githubURLParts               6.63   0.06    6.70
githubDetails                6.34   0.07    6.60
subgraphByDegree             6.23   0.12    6.42
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
get_bioc_data               24.85   0.28   25.19
firstInBioc                 17.59   0.30   17.94
biocDownloadStats           16.61   0.37   17.06
buildPkgDependencyDataFrame 13.29   0.33   13.69
pkgDepMetrics               12.40   0.41   12.92
pkgCombDependencyGain       12.17   0.59   13.07
buildPkgDependencyIgraph     5.99   0.06    6.06
inducedSubgraphByPkgs        5.68   0.14    5.85
githubURLParts               5.24   0.07    5.33
subgraphByDegree             5.16   0.15    5.33
biocPkgList                  5.00   0.11    5.12
githubDetails                4.98   0.13    5.36
getBiocVignette              4.98   0.06    5.11
* 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/BiocPkgTools.Rcheck/00check.log'
for details.

Installation output

BiocPkgTools.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/BiocPkgTools_1.6.0.tar.gz && rm -rf BiocPkgTools.buildbin-libdir && mkdir BiocPkgTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocPkgTools.buildbin-libdir BiocPkgTools_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL BiocPkgTools_1.6.0.zip && rm BiocPkgTools_1.6.0.tar.gz BiocPkgTools_1.6.0.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
100  272k  100  272k    0     0  4031k      0 --:--:-- --:--:-- --:--:-- 4402k

install for i386

* installing *source* package 'BiocPkgTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocPkgTools'
    finding HTML links ... done
    BiocPkgTools-cache                      html  
    BiocPkgTools                            html  
    CRANstatus                              html  
    biocBuildEmail                          html  
    biocBuildReport                         html  
    biocDownloadStats                       html  
    biocExplore                             html  
    biocPkgList                             html  
    buildPkgDependencyDataFrame             html  
    buildPkgDependencyIgraph                html  
    dataciteXMLGenerate                     html  
    dot-getDepGain                          html  
    firstInBioc                             html  
    generateBiocPkgDOI                      html  
    getBiocVignette                         html  
    getPackageInfo                          html  
    get_bioc_data                           html  
    githubDetails                           html  
    githubURLParts                          html  
    inducedSubgraphByPkgs                   html  
    pkgCombDependencyGain                   html  
    pkgDepImports                           html  
    pkgDepMetrics                           html  
    problemPage                             html  
    subgraphByDegree                        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 'BiocPkgTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocPkgTools' as BiocPkgTools_1.6.0.zip
* DONE (BiocPkgTools)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'BiocPkgTools' successfully unpacked and MD5 sums checked

Tests output

BiocPkgTools.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(BiocPkgTools)
Loading required package: htmlwidgets
> 
> test_check("BiocPkgTools")
trying URL 'https://bioconductor.org/packages/3.11/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1331857 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

== testthat results  ===========================================================
[ OK: 22 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  26.95    0.93   28.67

BiocPkgTools.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(BiocPkgTools)
Loading required package: htmlwidgets
> 
> test_check("BiocPkgTools")
trying URL 'https://bioconductor.org/packages/3.11/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1331857 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

== testthat results  ===========================================================
[ OK: 22 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  25.37    0.64   26.42

Example timings

BiocPkgTools.Rcheck/examples_i386/BiocPkgTools-Ex.timings

nameusersystemelapsed
biocBuildReport3.060.143.97
biocDownloadStats26.83 0.2527.50
biocPkgList8.460.138.87
buildPkgDependencyDataFrame17.36 0.2617.64
buildPkgDependencyIgraph7.720.057.78
firstInBioc25.87 0.2226.14
generateBiocPkgDOI000
getBiocVignette7.350.147.53
get_bioc_data35.17 0.1735.40
githubDetails6.340.076.60
githubURLParts6.630.066.70
inducedSubgraphByPkgs6.890.097.05
pkgCombDependencyGain12.75 0.5213.42
pkgDepImports0.150.000.16
pkgDepMetrics14.38 0.4414.98
problemPage000
subgraphByDegree6.230.126.42

BiocPkgTools.Rcheck/examples_x64/BiocPkgTools-Ex.timings

nameusersystemelapsed
biocBuildReport2.420.082.64
biocDownloadStats16.61 0.3717.06
biocPkgList5.000.115.12
buildPkgDependencyDataFrame13.29 0.3313.69
buildPkgDependencyIgraph5.990.066.06
firstInBioc17.59 0.3017.94
generateBiocPkgDOI000
getBiocVignette4.980.065.11
get_bioc_data24.85 0.2825.19
githubDetails4.980.135.36
githubURLParts5.240.075.33
inducedSubgraphByPkgs5.680.145.85
pkgCombDependencyGain12.17 0.5913.07
pkgDepImports0.180.000.17
pkgDepMetrics12.40 0.4112.92
problemPage000
subgraphByDegree5.160.155.33