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This page was generated on 2025-08-30 12:07 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 195/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.27.12  (landing page)
Sean Davis
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025)
git_url: https://git.bioconductor.org/packages/BiocPkgTools
git_branch: devel
git_last_commit: 68dd50d
git_last_commit_date: 2025-08-27 16:14:54 -0400 (Wed, 27 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  


CHECK results for BiocPkgTools on kjohnson3

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: 1.27.12
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_1.27.12.tar.gz
StartedAt: 2025-08-29 18:21:22 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 18:24:19 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 177.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocPkgTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.27.12.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BiocPkgTools.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocPkgTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocPkgTools’ version ‘1.27.12’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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_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       3.152 13.447  18.323
firstInBioc           5.354  0.143   6.235
get_bioc_data         5.071  0.174   5.944
biocDownloadStats     4.621  0.131   5.469
pkgCombDependencyGain 3.681  0.298  36.506
pkgDepMetrics         2.372  0.206  25.569
* 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-3.22-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/4.5-arm64/Resources/library’
* installing *source* package ‘BiocPkgTools’ ...
** this is package ‘BiocPkgTools’ version ‘1.27.12’
** 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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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/3.22/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1397518 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

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

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
 10.484   8.632  21.302 

Example timings

BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings

nameusersystemelapsed
activitySince0.0000.0010.000
anacondaDownloadStats1.0110.0121.426
biocBuildReport 3.15213.44718.323
biocDownloadStats4.6210.1315.469
biocMaintained1.5290.0592.259
biocPkgList0.5130.0140.717
biocPkgRanges0.0000.0010.000
biocRevDepEmail0.8050.0391.522
buildPkgDependencyDataFrame1.0830.0261.349
buildPkgDependencyIgraph0.5640.0150.681
class-dependencies2.1960.0712.272
firstInBioc5.3540.1436.235
generateBiocPkgDOI000
getBiocVignette0.4900.0200.837
getPkgYearsInBioc000
get_bioc_data5.0710.1745.944
get_cre_orcids0.0030.0000.004
githubDetails0.6400.1081.023
githubURLParts0.4930.0090.525
inducedSubgraphByPkgs1.7520.0532.011
latestPkgStats000
orcid_table0.0000.0010.000
pkgBiocDeps0.5180.0120.531
pkgBiocRevDeps0.6760.0120.688
pkgCombDependencyGain 3.681 0.29836.506
pkgDepImports0.0470.0000.047
pkgDepMetrics 2.372 0.20625.569
pkgDownloadRank0.7010.0561.521
pkgDownloadStats0.0120.0010.055
problemPage0.0000.0000.001
repositoryStats0.0290.0010.029
subgraphByDegree0.5110.0090.540