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This page was generated on 2021-10-23 14:06:53 -0400 (Sat, 23 Oct 2021).

CHECK results for BioPlex on merida1

To the developers/maintainers of the BioPlex package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioPlex.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 190/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioPlex 0.99.14  (landing page)
Ludwig Geistlinger
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/BioPlex
git_branch: master
git_last_commit: 4acc1ed
git_last_commit_date: 2021-08-31 14:55:42 -0400 (Tue, 31 Aug 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BioPlex
Version: 0.99.14
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioPlex.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioPlex_0.99.14.tar.gz
StartedAt: 2021-10-23 01:18:44 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 01:24:20 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 335.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BioPlex.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioPlex.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioPlex_0.99.14.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BioPlex.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioPlex/DESCRIPTION’ ... OK
* this is package ‘BioPlex’ version ‘0.99.14’
* 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 ‘BioPlex’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getCorum: no visible binding for global variable ‘Organism’
Undefined global functions or variables:
  Organism
* 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
ccleProteome2SummarizedExperiment 68.816  1.226  70.873
annotatePFAM                      23.003  1.051  25.212
mapSummarizedExperimentOntoGraph  10.523  0.396  11.084
bioplex2graph                      9.440  0.211   9.733
hasSubunit                         8.302  0.167   8.589
corum2graphlist                    7.528  0.178   7.930
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/BioPlex.Rcheck/00check.log’
for details.



Installation output

BioPlex.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BioPlex
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘BioPlex’ ...
** 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 (BioPlex)

Tests output


Example timings

BioPlex.Rcheck/BioPlex-Ex.timings

nameusersystemelapsed
annotatePFAM23.003 1.05125.212
bioplex2graph9.4400.2119.733
ccleProteome2SummarizedExperiment68.816 1.22670.873
corum2graphlist7.5280.1787.930
corum2list1.3420.0311.587
getBioPlex3.7940.0743.968
getBioplexProteome1.1460.0181.190
getCorum1.2940.0271.537
getGSE1224251.2840.0181.303
hasSubunit8.3020.1678.589
mapSummarizedExperimentOntoGraph10.523 0.39611.084