Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:11 -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 BioPlex on palomino3


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? 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 195/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioPlex 1.2.3  (landing page)
Ludwig Geistlinger
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/BioPlex
git_branch: RELEASE_3_15
git_last_commit: ba606c6
git_last_commit_date: 2022-06-13 16:13:53 -0400 (Mon, 13 Jun 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: BioPlex
Version: 1.2.3
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioPlex.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BioPlex_1.2.3.tar.gz
StartedAt: 2022-10-18 22:26:43 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 22:31:11 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 268.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BioPlex.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioPlex.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BioPlex_1.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/BioPlex.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 'BioPlex/DESCRIPTION' ... OK
* this is package 'BioPlex' version '1.2.3'
* 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 '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 43.25   2.41   60.26
annotatePFAM                      20.13   0.92   25.28
bioplex2graph                      7.89   0.20    8.14
mapSummarizedExperimentOntoGraph   6.75   0.23    7.06
corum2graphlist                    5.04   0.23    5.50
hasSubunit                         5.13   0.13    5.36
* 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/BioPlex.Rcheck/00check.log'
for details.



Installation output

BioPlex.Rcheck/00install.out

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


* installing to library 'F:/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
annotatePFAM20.13 0.9225.28
bioplex2graph7.890.208.14
ccleProteome2SummarizedExperiment43.25 2.4160.26
corum2graphlist5.040.235.50
corum2list0.370.070.67
getBioPlex1.890.152.28
getBioplexProteome0.280.030.34
getCorum0.290.130.55
getGSE1224250.410.030.52
getHEK293GenomeTrack1.000.031.48
hasSubunit5.130.135.36
mapSummarizedExperimentOntoGraph6.750.237.06