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This page was generated on 2022-03-18 11:08:22 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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

CHECK results for PubScore on riesling1


To the developers/maintainers of the PubScore package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PubScore.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 1491/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PubScore 1.7.0  (landing page)
Tiago Lubiana
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/PubScore
git_branch: master
git_last_commit: a2f4c91
git_last_commit_date: 2021-10-26 12:56:26 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PubScore
Version: 1.7.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PubScore.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PubScore_1.7.0.tar.gz
StartedAt: 2022-03-17 19:57:06 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 20:00:52 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 225.5 seconds
RetCode: 0
Status:   OK  
CheckDir: PubScore.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PubScore.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PubScore_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/PubScore.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PubScore/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PubScore' version '1.7.0'
* 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 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 LazyData ... 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            21.20   6.02   33.84
plot_literature_graph  0.54   0.00    5.67
plot_literature_score  0.49   0.00   24.83
get_literature_score   0.12   0.00    9.37
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/PubScore.Rcheck/00check.log'
for details.



Installation output

PubScore.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL PubScore
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/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
  converting help for package 'PubScore'
    finding HTML links ... done
    PubScore-class                          html  
    all_counts                              html  
    dot-getSimulation_test                  html  
    dot-query_pubmed                        html  
    gene2pubmed_db                          html  
    getScore                                html  
    get_all_counts                          html  
    get_literature_score                    html  
    heatmapViz                              html  
    hgcn_entrez_reference                   html  
    initialize-PubScore-method              html  
    networkViz                              html  
    plot_literature_graph                   html  
    plot_literature_score                   html  
    pubscore                                html  
    set_all_counts                          html  
    test_score                              html  
** 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)
Making 'packages.html' ... done

Tests output

PubScore.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 ~~~ 
[1] 1194.111
~~~ Initializing PubScore Object ~~~ 
~~~ Initializing PubScore Object ~~~ 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
  27.04    4.00   87.79 

Example timings

PubScore.Rcheck/PubScore-Ex.timings

nameusersystemelapsed
getScore0.830.083.11
get_all_counts0.450.002.95
get_literature_score0.120.009.37
heatmapViz0.210.002.24
networkViz0.420.002.39
plot_literature_graph0.540.005.67
plot_literature_score 0.49 0.0024.83
set_all_counts0.080.001.59
test_score21.20 6.0233.84