Package: PubScore

Version: 0.99.3

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_0.99.3.tar.gz

StartedAt: 2020-01-16 07:45:45 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:52:42 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 416.1 seconds

RetCode: 0

Status:  OK

CheckDir: PubScore.Rcheck

Warnings: 0

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### Running command:
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###   /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_0.99.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/PubScore.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘0.99.3’
* 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            59.435 40.829 106.873
plot_literature_score  1.244  0.036  19.953
plot_literature_graph  1.062  0.016   5.167
get_literature_score   0.312  0.011   7.742
* 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.

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### Running command:
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###   /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)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 
 71.281  42.516 194.748 

name	user	system	elapsed
getScore	1.422	0.092	3.203
get_all_counts	0.932	0.043	3.054
get_literature_score	0.312	0.011	7.742
heatmapViz	0.480	0.007	2.060
networkViz	0.773	0.005	2.344
plot_literature_graph	1.062	0.016	5.167
plot_literature_score	1.244	0.036	19.953
set_all_counts	0.170	0.015	1.597
test_score	59.435	40.829	106.873