Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-25 11:05:20 -0500 (Tue, 25 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
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 BioPlex on nebbiolo1


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 187/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioPlex 1.1.2  (landing page)
Ludwig Geistlinger
Snapshot Date: 2022-01-24 13:55:18 -0500 (Mon, 24 Jan 2022)
git_url: https://git.bioconductor.org/packages/BioPlex
git_branch: master
git_last_commit: 5653a0e
git_last_commit_date: 2021-10-29 12:27:07 -0500 (Fri, 29 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'SummarizedExperiment' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BioPlex
Version: 1.1.2
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:BioPlex.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings BioPlex_1.1.2.tar.gz
StartedAt: 2022-01-24 18:21:36 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-24 18:24:51 -0500 (Mon, 24 Jan 2022)
EllapsedTime: 195.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BioPlex.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:BioPlex.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings BioPlex_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/BioPlex.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioPlex/DESCRIPTION’ ... OK
* this is package ‘BioPlex’ version ‘1.1.2’
* 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 36.398  0.908  38.083
annotatePFAM                      15.042  0.469  16.237
bioplex2graph                      8.132  0.024   8.213
mapSummarizedExperimentOntoGraph   8.074  0.072   8.277
hasSubunit                         5.039  0.072   5.222
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/BioPlex.Rcheck/00check.log’
for details.



Installation output

BioPlex.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL BioPlex
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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
annotatePFAM15.042 0.46916.237
bioplex2graph8.1320.0248.213
ccleProteome2SummarizedExperiment36.398 0.90838.083
corum2graphlist4.0020.0684.939
corum2list0.2790.0120.403
getBioPlex1.6120.0161.782
getBioplexProteome0.2220.0000.250
getCorum0.3260.0040.443
getGSE1224250.6970.0040.701
getHEK293GenomeTrack0.3340.0121.324
hasSubunit5.0390.0725.222
mapSummarizedExperimentOntoGraph8.0740.0728.277