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This page was generated on 2025-10-04 10:01 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 917
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Package 35/229HostnameOS / ArchINSTALLBUILDCHECK
BiocPkgTools 1.27.12  (landing page)
Sean Davis
Snapshot Date: 2025-10-04 06:00 -0400 (Sat, 04 Oct 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)
teran2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  


CHECK results for BiocPkgTools on teran2

To the developers/maintainers of the BiocPkgTools package:
- 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: /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings BiocPkgTools_1.27.12.tar.gz
StartedAt: 2025-10-04 07:51:22 -0400 (Sat, 04 Oct 2025)
EndedAt: 2025-10-04 08:02:52 -0400 (Sat, 04 Oct 2025)
EllapsedTime: 690.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocPkgTools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings BiocPkgTools_1.27.12.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/BiocPkgTools.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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       7.290  6.651  10.671
pkgCombDependencyGain 8.054  0.100  10.092
pkgDepMetrics         4.971  0.036   6.910
get_bioc_data         2.437  0.051 105.825
firstInBioc           2.194  0.087 105.207
biocDownloadStats     1.591  0.061 104.479
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/BiocPkgTools.Rcheck/00check.log’
for details.


Installation output

BiocPkgTools.Rcheck/00install.out

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL BiocPkgTools
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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/3.21/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1397541 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 
 19.405   4.748  22.986 

Example timings

BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings

nameusersystemelapsed
activitySince000
anacondaDownloadStats1.7560.0432.441
biocBuildReport 7.290 6.65110.671
biocDownloadStats 1.591 0.061104.479
biocMaintained2.3110.0173.091
biocPkgList1.0080.0041.130
biocPkgRanges000
biocRevDepEmail1.4650.0242.154
buildPkgDependencyDataFrame1.6670.0091.820
buildPkgDependencyIgraph0.8380.0030.963
class-dependencies4.1690.1974.373
firstInBioc 2.194 0.087105.207
generateBiocPkgDOI000
getBiocVignette0.7620.0090.866
getPkgYearsInBioc000
get_bioc_data 2.437 0.051105.825
get_cre_orcids0.0070.0000.007
githubDetails1.0600.0611.356
githubURLParts0.9290.0091.059
inducedSubgraphByPkgs3.8040.0224.446
latestPkgStats000
orcid_table000
pkgBiocDeps0.7840.0210.806
pkgBiocRevDeps1.1360.0701.207
pkgCombDependencyGain 8.054 0.10010.092
pkgDepImports0.1120.0000.112
pkgDepMetrics4.9710.0366.910
pkgDownloadRank0.9630.0141.877
pkgDownloadStats0.1010.0010.127
problemPage000
repositoryStats0.0400.0010.042
subgraphByDegree0.8390.0070.964