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CHECK results for graphite on nebbiolo1

This page was generated on 2021-06-11 14:05:41 -0400 (Fri, 11 Jun 2021).

Package 808/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graphite 1.38.0  (landing page)
Gabriele Sales
Snapshot Date: 2021-06-10 06:50:12 -0400 (Thu, 10 Jun 2021)
URL: https://git.bioconductor.org/packages/graphite
Branch: RELEASE_3_13
Last Commit: 7517460
Last Changed Date: 2021-05-19 11:49:41 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
To the developers/maintainers of the graphite package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graphite.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.

Summary

Package: graphite
Version: 1.38.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:graphite.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings graphite_1.38.0.tar.gz
StartedAt: 2021-06-10 12:15:47 -0400 (Thu, 10 Jun 2021)
EndedAt: 2021-06-10 12:20:21 -0400 (Thu, 10 Jun 2021)
EllapsedTime: 274.5 seconds
RetCode: 0
Status:   OK  
CheckDir: graphite.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:graphite.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings graphite_1.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/graphite.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graphite/DESCRIPTION’ ... OK
* this is package ‘graphite’ version ‘1.38.0’
* 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 ‘graphite’ 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 ... OK
* 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
runClipper         14.599  0.412  18.363
convertIdentifiers  7.979  0.511   8.536
pathways            7.244  0.024   9.078
pathwayGraph        6.849  0.043   6.944
runTopologyGSA      4.776  0.048   6.326
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: OK


Installation output

graphite.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL graphite
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘graphite’ ...
** 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 (graphite)

Tests output

graphite.Rcheck/tests/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(graphite)
> 
> test_check("graphite")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 95 ]
> 
> proc.time()
   user  system elapsed 
 56.147   3.319 132.721 

Example timings

graphite.Rcheck/graphite-Ex.timings

nameusersystemelapsed
as.list.PathwayList1.1470.0841.231
buildPathway0.0090.0000.008
convertIdentifiers7.9790.5118.536
cytoscapePlot0.0010.0000.000
pathwayDatabases0.0090.0050.013
pathwayGraph6.8490.0436.944
pathways7.2440.0249.078
runClipper14.599 0.41218.363
runSPIA3.7390.3034.069
runTopologyGSA4.7760.0486.326