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This page was generated on 2021-06-18 14:05:55 -0400 (Fri, 18 Jun 2021).

CHECK results for psygenet2r on nebbiolo1

To the developers/maintainers of the psygenet2r package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/psygenet2r.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 1456/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psygenet2r 1.24.0  (landing page)
Alba Gutierrez-Sacristan
Snapshot Date: 2021-06-17 06:50:12 -0400 (Thu, 17 Jun 2021)
URL: https://git.bioconductor.org/packages/psygenet2r
Branch: RELEASE_3_13
Last Commit: 7a013f8
Last Changed Date: 2021-05-19 12:18:38 -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    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: psygenet2r
Version: 1.24.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:psygenet2r.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings psygenet2r_1.24.0.tar.gz
StartedAt: 2021-06-17 13:09:22 -0400 (Thu, 17 Jun 2021)
EndedAt: 2021-06-17 13:13:56 -0400 (Thu, 17 Jun 2021)
EllapsedTime: 274.3 seconds
RetCode: 0
Status:   OK  
CheckDir: psygenet2r.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:psygenet2r.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings psygenet2r_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/psygenet2r.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 ‘psygenet2r/DESCRIPTION’ ... OK
* this is package ‘psygenet2r’ version ‘1.24.0’
* 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 ‘psygenet2r’ 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 ... NOTE
Namespace in Imports field not imported from: ‘GO.db’
  All declared Imports should be used.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.category_plot: no visible binding for global variable ‘category’
.category_plot: no visible binding for global variable ‘value’
.category_plot: no visible binding for global variable ‘variable’
.gene_plot: no visible binding for global variable ‘gene’
.gene_plot: no visible binding for global variable ‘value’
.gene_plot: no visible binding for global variable ‘variable’
.index_plot: no visible binding for global variable ‘Category’
.index_plot: no visible binding for global variable ‘value’
.index_plot: no visible binding for global variable ‘variable’
.pie_plot: no visible global function definition for ‘pie’
ListPsyGeNETIds: no visible global function definition for ‘read.csv’
disGenetCurated: no visible global function definition for ‘read.csv’
enrichedPD : <anonymous>: no visible global function definition for
  ‘phyper’
getUMLs: no visible global function definition for ‘read.csv’
jaccardEstimation: no visible binding for global variable ‘universe’
multipleInput: no visible global function definition for ‘new’
pantherGraphic: no visible binding for global variable ‘Var1’
pantherGraphic: no visible binding for global variable ‘perc’
pantherGraphic: no visible binding for global variable ‘diseases’
plot_pmids_barplot: no visible binding for global variable
  ‘c2.DiseaseName’
plot_pmids_barplot: no visible binding for global variable
  ‘c0.Number_of_Abstracts’
plot_pmids_barplot: no visible binding for global variable
  ‘c1.Gene_Symbol’
plot_psy_heatmap: no visible binding for global variable
  ‘c2.PsychiatricDisorder’
plot_psy_heatmap: no visible binding for global variable
  ‘c1.Gene_Symbol’
plot_psy_heatmap: no visible binding for global variable ‘value’
plot_psy_heatmapDisease: no visible binding for global variable
  ‘c2.DiseaseName’
plot_psy_heatmapDisease: no visible binding for global variable
  ‘c1.Gene_Symbol’
plot_psy_heatmapDisease: no visible binding for global variable
  ‘c0.Score’
plot_psy_heatmapGenes: no visible binding for global variable
  ‘c1.Gene_Symbol’
plot_psy_heatmapGenes: no visible binding for global variable
  ‘c2.DiseaseName’
plot_psy_heatmapGenes: no visible binding for global variable
  ‘c0.Score’
psyGenDisId: no visible global function definition for ‘read.csv’
psyPanther: no visible global function definition for ‘read.csv’
psygenetAll: no visible global function definition for ‘read.csv’
psygenetDisease: no visible global function definition for ‘read.csv’
psygenetDisease: no visible global function definition for ‘new’
psygenetDiseaseSentences: no visible global function definition for
  ‘read.csv’
psygenetDiseaseSentences: no visible global function definition for
  ‘new’
psygenetGene: no visible global function definition for ‘read.csv’
psygenetGene: no visible global function definition for ‘new’
psygenetGeneSentences: no visible global function definition for
  ‘read.csv’
psygenetGeneSentences: no visible global function definition for ‘new’
singleInput: no visible global function definition for ‘combn’
singleInput: no visible global function definition for ‘new’
singleInput.genes: no visible global function definition for ‘new’
topAnatEnrichment: no visible binding for global variable ‘database’
topAnatEnrichment: no visible global function definition for
  ‘read.delim’
plot,JaccardIndexPsy-ANY: no visible binding for global variable
  ‘Disease1’
plot,JaccardIndexPsy-ANY: no visible binding for global variable
  ‘Disease2’
plot,JaccardIndexPsy-ANY: no visible binding for global variable
  ‘JaccardIndex’
plot,JaccardIndexPsy-ANY: no visible binding for global variable
  ‘value’
plot,JaccardIndexPsy-ANY: no visible binding for global variable
  ‘variable’
Undefined global functions or variables:
  Category Disease1 Disease2 JaccardIndex Var1 c0.Number_of_Abstracts
  c0.Score c1.Gene_Symbol c2.DiseaseName c2.PsychiatricDisorder
  category combn database diseases gene new perc phyper pie read.csv
  read.delim universe value variable
Consider adding
  importFrom("graphics", "pie")
  importFrom("methods", "new")
  importFrom("stats", "phyper")
  importFrom("utils", "combn", "read.csv", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
psygenetGeneSentences   0.306  0.028  35.574
pantherGraphic-methods  0.231  0.016   6.862
enrichedPD-methods      0.076  0.004   7.135
psygenetDisease-methods 0.052  0.004   5.648
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/psygenet2r.Rcheck/00check.log’
for details.



Installation output

psygenet2r.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL psygenet2r
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘psygenet2r’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (psygenet2r)

Tests output

psygenet2r.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(psygenet2r)
> 
> test_check("psygenet2r")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (4)

[ FAIL 0 | WARN 0 | SKIP 4 | PASS 18 ]
> 
> proc.time()
   user  system elapsed 
  6.300   0.281  90.112 

Example timings

psygenet2r.Rcheck/psygenet2r-Ex.timings

nameusersystemelapsed
JaccardIndexPsy-class0.2260.0054.954
enrichedPD-methods0.0760.0047.135
extract0.0040.0000.005
extractSentences0.0040.0000.003
getUMLs-methods0.0390.0043.930
jaccardEstimation-methods0.4780.0034.800
ndisease0.0020.0000.001
ngene0.0020.0000.001
pantherGraphic-methods0.2310.0166.862
plot-DataGeNET.Psy-ANY-method0.0460.0310.077
plot-JaccardIndexPsy-ANY-method000
psygenetDisease-methods0.0520.0045.648
psygenetDiseaseSentences0.0310.0044.067
psygenetGene-methods0.0440.0003.932
psygenetGeneSentences 0.306 0.02835.574
qr0.0000.0010.001
topAnatEnrichment-methods000
universe0.0010.0040.005