Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-17 11:06:53 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 riesling1


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 187/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioPlex 1.1.2  (landing page)
Ludwig Geistlinger
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 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: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioPlex.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BioPlex_1.1.2.tar.gz
StartedAt: 2022-01-16 18:26:44 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 18:29:57 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 192.4 seconds
RetCode: 0
Status:   OK  
CheckDir: BioPlex.Rcheck
Warnings: 0

Command output

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


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BioPlex.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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 34.84   2.34   37.91
annotatePFAM                      16.05   0.97   17.93
bioplex2graph                      6.46   0.17    6.68
mapSummarizedExperimentOntoGraph   5.47   0.44    6.00
corum2graphlist                    4.88   0.30    5.39
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/BioPlex.Rcheck/00check.log'
for details.



Installation output

BioPlex.Rcheck/00install.out

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


* installing to library 'D:/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
  converting help for package 'BioPlex'
    finding HTML links ... done
    annotatePFAM                            html  
    finding level-2 HTML links ... done

    bioplex2graph                           html  
    ccleProteome2SummarizedExperiment       html  
    corum2graphlist                         html  
    corum2list                              html  
    getBioPlex                              html  
    getBioplexProteome                      html  
    getCorum                                html  
    getGSE122425                            html  
    getHEK293GenomeTrack                    html  
    hasSubunit                              html  
    mapSummarizedExperimentOntoGraph        html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'phenoTest' is missing or broken
 done

Tests output


Example timings

BioPlex.Rcheck/BioPlex-Ex.timings

nameusersystemelapsed
annotatePFAM16.05 0.9717.93
bioplex2graph6.460.176.68
ccleProteome2SummarizedExperiment34.84 2.3437.91
corum2graphlist4.880.305.39
corum2list0.340.010.59
getBioPlex1.720.131.92
getBioplexProteome0.270.050.38
getCorum0.330.060.50
getGSE1224250.450.030.48
getHEK293GenomeTrack0.530.030.77
hasSubunit4.310.114.56
mapSummarizedExperimentOntoGraph5.470.446.00