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This page was generated on 2024-03-26 14:51:26 -0400 (Tue, 26 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
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

Package 27/425HostnameOS / ArchINSTALLBUILDCHECK
BioPlex 1.9.0  (landing page)
Ludwig Geistlinger
Snapshot Date: 2024-03-26 07:30:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/BioPlex
git_branch: devel
git_last_commit: 3e9f88f
git_last_commit_date: 2023-10-24 09:23:48 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

CHECK results for BioPlex on nebbiolo1


To the developers/maintainers of the BioPlex package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BioPlex
Version: 1.9.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BioPlex.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BioPlex_1.9.0.tar.gz
StartedAt: 2024-03-26 11:15:30 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 11:21:47 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 377.0 seconds
RetCode: 0
Status:   OK  
CheckDir: BioPlex.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BioPlex.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BioPlex_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/BioPlex.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BioPlex/DESCRIPTION’ ... OK
* this is package ‘BioPlex’ version ‘1.9.0’
* 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 code 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 loading without being on the library search path ... 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 35.919  2.013  38.260
annotatePFAM                      14.189  0.995  21.923
hasSubunit                         6.366  0.758   7.388
mapSummarizedExperimentOntoGraph   6.105  0.783   7.027
corum2graphlist                    5.864  0.619   6.770
bioplex2graph                      6.232  0.156   6.452
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/BioPlex.Rcheck/00check.log’
for details.


Installation output

BioPlex.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BioPlex
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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
annotatePFAM14.189 0.99521.923
bioplex2graph6.2320.1566.452
ccleProteome2SummarizedExperiment35.919 2.01338.260
corum2graphlist5.8640.6196.770
corum2list1.5590.2162.067
getBioPlex1.5210.1041.715
getBioplexProteome0.2000.0200.248
getCorum1.7000.2002.196
getGSE1224250.5980.0670.667
getHEK293GenomeTrack0.2850.0480.540
hasSubunit6.3660.7587.388
mapSummarizedExperimentOntoGraph6.1050.7837.027