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CHECK report for PubScore on machv2

This page was generated on 2020-10-17 11:59:18 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE PubScore PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1376/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PubScore 1.0.0
Tiago Lubiana
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/PubScore
Branch: RELEASE_3_11
Last Commit: 7ac3665
Last Changed Date: 2020-04-27 15:32:54 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PubScore
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PubScore.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PubScore_1.0.0.tar.gz
StartedAt: 2020-10-17 04:10:48 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:16:09 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 320.4 seconds
RetCode: 0
Status:  OK 
CheckDir: PubScore.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PubScore.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PubScore_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/PubScore.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PubScore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PubScore’ version ‘1.0.0’
* 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 ‘PubScore’ 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
get_literature_score: no visible binding for global variable
  ‘gene2pubmed_db’
get_literature_score: no visible binding for global variable
  ‘hgcn_entrez_reference’
get_sum_of_weights: no visible binding for global variable ‘Genes’
get_sum_of_weights: no visible binding for global variable ‘Topic’
plot_literature_score: no visible binding for global variable ‘Genes’
plot_literature_score: no visible binding for global variable ‘Topic’
plot_literature_score: no visible binding for global variable
  ‘number_of_articles’
show,PubScore: no visible binding for global variable ‘pub’
Undefined global functions or variables:
  Genes Topic gene2pubmed_db hgcn_entrez_reference number_of_articles
  pub
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
test_score            41.616 11.516  60.720
plot_literature_score  1.013  0.014  25.282
plot_literature_graph  0.657  0.008   7.220
get_literature_score   0.272  0.007   9.709
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/PubScore.Rcheck/00check.log’
for details.



Installation output

PubScore.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PubScore
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘PubScore’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (PubScore)

Tests output

PubScore.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(PubScore)
> 
> test_check("PubScore")
~~~ Initializing PubScore Object ~~~ 
~~~ Initializing PubScore Object ~~~ 
~~~ Initializing PubScore Object ~~~ 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 51.855  12.189 144.156 

Example timings

PubScore.Rcheck/PubScore-Ex.timings

nameusersystemelapsed
getScore1.0020.0583.174
get_all_counts0.6260.0143.249
get_literature_score0.2720.0079.709
heatmapViz0.3590.0042.567
networkViz0.5060.0052.874
plot_literature_graph0.6570.0087.220
plot_literature_score 1.013 0.01425.282
set_all_counts0.1510.0101.914
test_score41.61611.51660.720