Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:09 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 palomino3


To the developers/maintainers of the BiocPkgTools package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 167/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.14.1  (landing page)
Sean Davis
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/BiocPkgTools
git_branch: RELEASE_3_15
git_last_commit: 194b8cc
git_last_commit_date: 2022-08-16 12:14:09 -0400 (Tue, 16 Aug 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BiocPkgTools
Version: 1.14.1
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocPkgTools.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BiocPkgTools_1.14.1.tar.gz
StartedAt: 2022-10-18 22:21:34 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 22:29:56 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 502.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocPkgTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocPkgTools.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BiocPkgTools_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/BiocPkgTools.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BiocPkgTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiocPkgTools' version '1.14.1'
* 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 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'BiocManager:::.repositories' 'BiocManager:::.repositories_bioc'
  '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       3.26   3.86  126.22
get_bioc_data         6.39   0.50    7.00
firstInBioc           6.25   0.45    6.72
pkgCombDependencyGain 5.85   0.50    6.41
biocDownloadStats     5.75   0.39    6.76
pkgDepMetrics         5.28   0.64    5.95
class-dependencies    5.05   0.14    5.19
githubDetails         1.17   0.11    7.83
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.15-bioc/meat/BiocPkgTools.Rcheck/00check.log'
for details.



Installation output

BiocPkgTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BiocPkgTools
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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/3.15/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1304099 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
  32.54    5.21  153.51 

Example timings

BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings

nameusersystemelapsed
anacondaDownloadStats1.860.062.35
biocBuildReport 3.26 3.86126.22
biocDownloadStats5.750.396.76
biocMaintained1.070.111.19
biocPkgList1.420.091.52
biocPkgRanges0.000.020.01
biocRevDepEmail1.400.172.11
buildPkgDependencyDataFrame2.720.192.95
buildPkgDependencyIgraph1.060.191.27
class-dependencies5.050.145.19
firstInBioc6.250.456.72
generateBiocPkgDOI000
getBiocVignette1.580.061.80
get_bioc_data6.390.507.00
githubDetails1.170.117.83
githubURLParts0.970.061.17
inducedSubgraphByPkgs1.210.071.32
pkgCombDependencyGain5.850.506.41
pkgDepImports0.190.020.20
pkgDepMetrics5.280.645.95
pkgDownloadStats0.020.000.04
problemPage000
subgraphByDegree1.110.061.18