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This page was generated on 2021-08-04 12:04:49 -0400 (Wed, 04 Aug 2021).

CHECK results for BiocPkgTools on riesling1

To the developers/maintainers of the BiocPkgTools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocPkgTools.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 164/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.11.6  (landing page)
Sean Davis
Snapshot Date: 2021-08-03 14:50:07 -0400 (Tue, 03 Aug 2021)
URL: https://git.bioconductor.org/packages/BiocPkgTools
Branch: master
Last Commit: 428d110
Last Changed Date: 2021-07-29 17:51:54 -0400 (Thu, 29 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BiocPkgTools
Version: 1.11.6
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocPkgTools.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BiocPkgTools_1.11.6.tar.gz
StartedAt: 2021-08-03 23:30:16 -0400 (Tue, 03 Aug 2021)
EndedAt: 2021-08-03 23:40:45 -0400 (Tue, 03 Aug 2021)
EllapsedTime: 629.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocPkgTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocPkgTools.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BiocPkgTools_1.11.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/BiocPkgTools.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '1.11.6'
* 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
Unexported objects imported by ':::' calls:
  'BiocManager:::.repositories' 'BiocManager:::.version_bioc'
  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               51.56  38.64   90.34
firstInBioc                 43.16  28.80   72.04
biocDownloadStats           39.81  23.06   63.00
buildPkgDependencyDataFrame  9.94   0.14   10.11
pkgCombDependencyGain        9.28   0.30    9.76
pkgDepMetrics                8.24   0.33    8.66
biocBuildReport              6.21   0.14    6.68
inducedSubgraphByPkgs        5.50   0.03    5.55
githubDetails                5.24   0.03   10.59
buildPkgDependencyIgraph     5.08   0.08    5.17
biocMaintained               5.09   0.05    5.28
subgraphByDegree             5.07   0.05    5.13
githubURLParts               5.06   0.05    5.13
getBiocVignette              4.95   0.09    5.21
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
get_bioc_data               30.13  10.01   40.25
biocDownloadStats           25.47  11.64   37.21
firstInBioc                 26.15  10.69   36.94
pkgCombDependencyGain        7.86   0.40    8.86
buildPkgDependencyDataFrame  7.51   0.19    7.73
biocBuildReport              7.14   0.11    7.48
pkgDepMetrics                6.83   0.42    7.30
githubURLParts               4.14   0.10    6.25
githubDetails                3.90   0.10    8.49
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/BiocPkgTools.Rcheck/00check.log'
for details.



Installation output

BiocPkgTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BiocPkgTools_1.11.6.tar.gz && rm -rf BiocPkgTools.buildbin-libdir && mkdir BiocPkgTools.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocPkgTools.buildbin-libdir BiocPkgTools_1.11.6.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BiocPkgTools_1.11.6.zip && rm BiocPkgTools_1.11.6.tar.gz BiocPkgTools_1.11.6.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  280k  100  280k    0     0  1895k      0 --:--:-- --:--:-- --:--:-- 1895k

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  
    anacondaDownloadStats                   html  
    biocBuildEmail                          html  
    biocBuildReport                         html  
    biocDownloadStats                       html  
    biocExplore                             html  
    biocMaintained                          html  
    biocPkgList                             html  
    biocPkgRanges                           html  
    buildPkgDependencyDataFrame             html  
    buildPkgDependencyIgraph                html  
    class-dependencies                      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  
    pkgDownloadStats                        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_1.11.6.zip
* DONE (BiocPkgTools)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'BiocPkgTools' successfully unpacked and MD5 sums checked

Tests output

BiocPkgTools.Rcheck/tests_i386/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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(BiocPkgTools)
Loading required package: htmlwidgets
> 
> test_check("BiocPkgTools")
trying URL 'https://bioconductor.org/packages/3.14/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1297215 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 20 ]
> 
> proc.time()
   user  system elapsed 
  19.18    0.40   20.15 

BiocPkgTools.Rcheck/tests_x64/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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(BiocPkgTools)
Loading required package: htmlwidgets
> 
> test_check("BiocPkgTools")
trying URL 'https://bioconductor.org/packages/3.14/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1297215 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 20 ]
> 
> proc.time()
   user  system elapsed 
  15.65    0.50   16.64 

Example timings

BiocPkgTools.Rcheck/examples_i386/BiocPkgTools-Ex.timings

nameusersystemelapsed
anacondaDownloadStats0.470.031.17
biocBuildReport6.210.146.68
biocDownloadStats39.8123.0663.00
biocMaintained5.090.055.28
biocPkgList4.910.085.00
biocPkgRanges000
buildPkgDependencyDataFrame 9.94 0.1410.11
buildPkgDependencyIgraph5.080.085.17
class-dependencies2.970.093.07
firstInBioc43.1628.8072.04
generateBiocPkgDOI000
getBiocVignette4.950.095.21
get_bioc_data51.5638.6490.34
githubDetails 5.24 0.0310.59
githubURLParts5.060.055.13
inducedSubgraphByPkgs5.500.035.55
pkgCombDependencyGain9.280.309.76
pkgDepImports0.120.010.14
pkgDepMetrics8.240.338.66
pkgDownloadStats0.010.000.04
problemPage000
subgraphByDegree5.070.055.13

BiocPkgTools.Rcheck/examples_x64/BiocPkgTools-Ex.timings

nameusersystemelapsed
anacondaDownloadStats0.460.061.02
biocBuildReport7.140.117.48
biocDownloadStats25.4711.6437.21
biocMaintained3.750.063.96
biocPkgList3.880.104.00
biocPkgRanges000
buildPkgDependencyDataFrame7.510.197.73
buildPkgDependencyIgraph3.910.114.03
class-dependencies3.080.213.30
firstInBioc26.1510.6936.94
generateBiocPkgDOI000
getBiocVignette3.640.163.89
get_bioc_data30.1310.0140.25
githubDetails3.900.108.49
githubURLParts4.140.106.25
inducedSubgraphByPkgs3.890.074.00
pkgCombDependencyGain7.860.408.86
pkgDepImports0.140.000.14
pkgDepMetrics6.830.427.30
pkgDownloadStats0.000.000.03
problemPage000
subgraphByDegree3.840.043.91