Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 186/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.23.1  (landing page)
Sean Davis
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/BiocPkgTools
git_branch: devel
git_last_commit: 373264c
git_last_commit_date: 2024-05-22 17:04:07 -0400 (Wed, 22 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for BiocPkgTools on merida1

To the developers/maintainers of the BiocPkgTools package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BiocPkgTools
Version: 1.23.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocPkgTools_1.23.1.tar.gz
StartedAt: 2024-06-10 00:24:09 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 00:38:51 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 881.6 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocPkgTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocPkgTools_1.23.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiocPkgTools.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocPkgTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocPkgTools’ version ‘1.23.1’
* 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 for sufficient/correct file permissions ... 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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:::.repositories_base’
  ‘BiocManager:::.repositories_bioc’
  ‘BiocManager:::.repository_container_version’
  ‘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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
biocBuildReport             16.246 68.251 107.242
get_bioc_data               22.266  1.982  56.016
firstInBioc                 20.320  1.040  48.524
biocDownloadStats           18.502  0.606  20.610
pkgCombDependencyGain       14.363  0.616  17.222
pkgDepMetrics               12.576  0.304  14.027
class-dependencies          12.326  0.478  26.633
inducedSubgraphByPkgs        7.891  1.897  24.692
biocMaintained               6.008  0.173   7.254
buildPkgDependencyDataFrame  5.137  0.116   6.961
biocRevDepEmail              4.118  0.171   8.564
pkgBiocRevDeps               3.695  0.233   8.304
githubDetails                2.847  0.672  13.268
buildPkgDependencyIgraph     2.645  0.063   5.274
getBiocVignette              2.426  0.263   6.607
pkgBiocDeps                  2.461  0.170   6.425
githubURLParts               2.186  0.226   5.257
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiocPkgTools.Rcheck/00check.log’
for details.


Installation output

BiocPkgTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocPkgTools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘BiocPkgTools’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (BiocPkgTools)

Tests output

BiocPkgTools.Rcheck/tests/testthat.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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/3.20/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1305410 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 27 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
 63.079  58.786 192.667 

Example timings

BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings

nameusersystemelapsed
activitySince0.0010.0010.001
anacondaDownloadStats3.2180.0763.947
biocBuildReport 16.246 68.251107.242
biocDownloadStats18.502 0.60620.610
biocMaintained6.0080.1737.254
biocPkgList2.5260.0452.952
biocPkgRanges0.0010.0010.001
biocRevDepEmail4.1180.1718.564
buildPkgDependencyDataFrame5.1370.1166.961
buildPkgDependencyIgraph2.6450.0635.274
class-dependencies12.326 0.47826.633
firstInBioc20.320 1.04048.524
generateBiocPkgDOI0.0000.0000.001
getBiocVignette2.4260.2636.607
get_bioc_data22.266 1.98256.016
get_cre_orcids0.0180.0030.052
githubDetails 2.847 0.67213.268
githubURLParts2.1860.2265.257
inducedSubgraphByPkgs 7.891 1.89724.692
latestPkgStats0.0000.0010.001
orcid_table0.0010.0010.001
pkgBiocDeps2.4610.1706.425
pkgBiocRevDeps3.6950.2338.304
pkgCombDependencyGain14.363 0.61617.222
pkgDepImports0.4520.0150.548
pkgDepMetrics12.576 0.30414.027
pkgDownloadRank3.2760.2814.381
pkgDownloadStats0.0670.0060.161
problemPage0.0000.0000.001
repositoryStats0.1080.0100.147
subgraphByDegree2.4340.0842.798