Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:51 -0400 (Fri, 15 Oct 2021).

CHECK results for rrvgo on nebbiolo1

To the developers/maintainers of the rrvgo package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rrvgo.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 1633/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rrvgo 1.4.4  (landing page)
Sergi Sayols
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/rrvgo
git_branch: RELEASE_3_13
git_last_commit: 60a1114
git_last_commit_date: 2021-07-28 10:44:24 -0400 (Wed, 28 Jul 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    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: rrvgo
Version: 1.4.4
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:rrvgo.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings rrvgo_1.4.4.tar.gz
StartedAt: 2021-10-14 11:25:28 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:31:58 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 389.8 seconds
RetCode: 0
Status:   OK  
CheckDir: rrvgo.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:rrvgo.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings rrvgo_1.4.4.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/rrvgo.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rrvgo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rrvgo’ version ‘1.4.4’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rrvgo’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘GOSemSim:::getAncestors’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
scatterPlot: no visible binding for global variable ‘V1’
scatterPlot: no visible binding for global variable ‘V2’
scatterPlot: no visible binding for global variable ‘parentTerm’
scatterPlot: no visible binding for global variable ‘parent’
Undefined global functions or variables:
  V1 V2 parent parentTerm
* 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
wordcloudPlot      43.332  0.148  43.483
scatterPlot        43.146  0.160  43.309
reduceSimMatrix    42.259  0.127  42.388
heatmapPlot        41.313  0.573  41.887
calculateSimMatrix 38.532  0.856  39.395
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/rrvgo.Rcheck/00check.log’
for details.



Installation output

rrvgo.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL rrvgo
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘rrvgo’ ...
** 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 (rrvgo)

Tests output

rrvgo.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(rrvgo)

> 
> test_check("rrvgo")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 88.548   1.103  89.643 

Example timings

rrvgo.Rcheck/rrvgo-Ex.timings

nameusersystemelapsed
calculateSimMatrix38.532 0.85639.395
gg_color_hue000
heatmapPlot41.313 0.57341.887
reduceSimMatrix42.259 0.12742.388
scatterPlot43.146 0.16043.309
treemapPlot000
wordcloudPlot43.332 0.14843.483