Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-09 12:04 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 194/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.27.9  (landing page)
Sean Davis
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/BiocPkgTools
git_branch: devel
git_last_commit: 0a55068
git_last_commit_date: 2025-07-15 14:23:40 -0400 (Tue, 15 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for BiocPkgTools on nebbiolo2

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: 1.27.9
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BiocPkgTools_1.27.9.tar.gz
StartedAt: 2025-08-08 20:26:52 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 20:32:35 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 343.4 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocPkgTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BiocPkgTools_1.27.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BiocPkgTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocPkgTools’ version ‘1.27.9’
* 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       14.304  8.257  17.893
firstInBioc           20.488  0.534  26.927
get_bioc_data         13.782  0.782  15.928
biocDownloadStats     10.918  0.311  11.768
pkgCombDependencyGain 10.253  0.465  18.822
pkgDepMetrics          7.919  0.301  16.355
class-dependencies     5.500  0.188   5.688
inducedSubgraphByPkgs  4.330  0.054   5.002
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/BiocPkgTools.Rcheck/00check.log’
for details.


Installation output

BiocPkgTools.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BiocPkgTools’ ...
** this is package ‘BiocPkgTools’ version ‘1.27.9’
** 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 
 28.620   5.204  32.305 

Example timings

BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings

nameusersystemelapsed
activitySince0.0010.0000.001
anacondaDownloadStats2.3790.0462.608
biocBuildReport14.304 8.25717.893
biocDownloadStats10.918 0.31111.768
biocMaintained3.5820.0594.843
biocPkgList1.1960.0091.331
biocPkgRanges000
biocRevDepEmail2.3140.0562.895
buildPkgDependencyDataFrame2.9100.0423.222
buildPkgDependencyIgraph1.2070.0071.366
class-dependencies5.5000.1885.688
firstInBioc20.488 0.53426.927
generateBiocPkgDOI000
getBiocVignette1.5860.0221.992
getPkgYearsInBioc0.0010.0000.000
get_bioc_data13.782 0.78215.928
get_cre_orcids0.0080.0010.008
githubDetails1.5060.1021.858
githubURLParts1.1510.0501.335
inducedSubgraphByPkgs4.3300.0545.002
latestPkgStats000
orcid_table0.0010.0000.000
pkgBiocDeps1.2420.0181.261
pkgBiocRevDeps1.6340.0071.642
pkgCombDependencyGain10.253 0.46518.822
pkgDepImports0.1730.0020.175
pkgDepMetrics 7.919 0.30116.355
pkgDownloadRank1.7210.0432.051
pkgDownloadStats0.0670.0000.173
problemPage0.0000.0000.001
repositoryStats0.0560.0000.057
subgraphByDegree1.1530.0061.317