Back to Build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-05-26 06:18:04 -0000 (Fri, 26 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4254
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

CHECK results for BiocPkgTools on kunpeng2


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 181/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.19.1  (landing page)
Sean Davis
Snapshot Date: 2023-05-25 13:29:39 -0000 (Thu, 25 May 2023)
git_url: https://git.bioconductor.org/packages/BiocPkgTools
git_branch: devel
git_last_commit: f4237b8
git_last_commit_date: 2023-05-03 20:14:01 -0000 (Wed, 03 May 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

Summary

Package: BiocPkgTools
Version: 1.19.1
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings BiocPkgTools_1.19.1.tar.gz
StartedAt: 2023-05-26 04:01:17 -0000 (Fri, 26 May 2023)
EndedAt: 2023-05-26 04:07:35 -0000 (Fri, 26 May 2023)
EllapsedTime: 378.5 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocPkgTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings BiocPkgTools_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BiocPkgTools.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘BiocPkgTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocPkgTools’ version ‘1.19.1’
* 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 ... 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
* 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
get_bioc_data               12.293  0.259  15.517
firstInBioc                 11.602  0.251  12.329
biocDownloadStats            9.246  0.152  10.108
pkgCombDependencyGain        8.490  0.223  16.876
class-dependencies           7.786  0.172   7.975
pkgDepMetrics                7.041  0.297  16.426
biocBuildReport              3.926  2.077   5.562
buildPkgDependencyDataFrame  2.557  0.021   7.302
inducedSubgraphByPkgs        1.246  0.088   5.660
biocRevDepEmail              1.263  0.020   7.357
getBiocVignette              1.179  0.028   7.846
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘BiocPkgTools.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/BiocPkgTools.Rcheck/00check.log’
for details.



Installation output

BiocPkgTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL BiocPkgTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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/3.18/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1305440 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
 33.304   2.495  48.868 

Example timings

BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings

nameusersystemelapsed
activitySince0.0010.0000.000
anacondaDownloadStats1.5080.1744.346
biocBuildReport3.9262.0775.562
biocDownloadStats 9.246 0.15210.108
biocMaintained1.3640.0124.574
biocPkgList1.4610.0244.120
biocPkgRanges0.0010.0000.000
biocRevDepEmail1.2630.0207.357
buildPkgDependencyDataFrame2.5570.0217.302
buildPkgDependencyIgraph1.2390.0122.538
class-dependencies7.7860.1727.975
firstInBioc11.602 0.25112.329
generateBiocPkgDOI0.0000.0000.001
getBiocVignette1.1790.0287.846
get_bioc_data12.293 0.25915.517
get_cre_orcids0.0080.0000.008
githubDetails1.5840.0634.945
githubURLParts1.2080.0404.236
inducedSubgraphByPkgs1.2460.0885.660
latestPkgStats000
orcid_table000
pkgBiocDeps0.1200.0050.820
pkgCombDependencyGain 8.490 0.22316.876
pkgDepImports0.2570.0000.257
pkgDepMetrics 7.041 0.29716.426
pkgDownloadRank1.1770.0582.139
pkgDownloadStats0.0280.0040.633
problemPage0.0010.0000.000
repositoryStats0.0860.0000.779
subgraphByDegree1.2610.0084.003