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This page was generated on 2024-02-28 11:38:06 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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

Package 1610/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psygenet2r 1.34.1  (landing page)
Alba Gutierrez-Sacristan
Snapshot Date: 2024-02-27 14:05:07 -0500 (Tue, 27 Feb 2024)
git_url: https://git.bioconductor.org/packages/psygenet2r
git_branch: RELEASE_3_18
git_last_commit: 1dce02c
git_last_commit_date: 2024-01-15 12:27:41 -0500 (Mon, 15 Jan 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for psygenet2r on lconway


To the developers/maintainers of the psygenet2r package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: psygenet2r
Version: 1.34.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:psygenet2r.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings psygenet2r_1.34.1.tar.gz
StartedAt: 2024-02-27 22:33:08 -0500 (Tue, 27 Feb 2024)
EndedAt: 2024-02-27 22:38:29 -0500 (Tue, 27 Feb 2024)
EllapsedTime: 320.8 seconds
RetCode: 0
Status:   OK  
CheckDir: psygenet2r.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:psygenet2r.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings psygenet2r_1.34.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/psygenet2r.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psygenet2r/DESCRIPTION’ ... OK
* this is package ‘psygenet2r’ version ‘1.34.1’
* 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
JaccardIndexPsy-class     0.592  0.015   9.876
pantherGraphic-methods    0.287  0.022   7.079
psygenetGeneSentences     0.252  0.035  37.159
enrichedPD-methods        0.075  0.011   9.900
jaccardEstimation-methods 0.074  0.009   5.340
psygenetDisease-methods   0.043  0.008   6.027
* 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
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/psygenet2r.Rcheck/00check.log’
for details.



Installation output

psygenet2r.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL psygenet2r
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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")
[ FAIL 0 | WARN 0 | SKIP 4 | PASS 18 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• empty test (4): 'test_basic_disease.R:20:1', 'test_basic_disease.R:25:1',
  'test_basic_gene.R:18:1', 'test_basic_gene.R:22:1'

[ FAIL 0 | WARN 0 | SKIP 4 | PASS 18 ]
> 
> proc.time()
   user  system elapsed 
  7.189   0.515  90.458 

Example timings

psygenet2r.Rcheck/psygenet2r-Ex.timings

nameusersystemelapsed
JaccardIndexPsy-class0.5920.0159.876
enrichedPD-methods0.0750.0119.900
extract0.0050.0020.007
extractSentences0.0030.0010.005
getUMLs-methods0.0320.0044.831
jaccardEstimation-methods0.0740.0095.340
ndisease0.0010.0020.002
ngene0.0010.0020.003
pantherGraphic-methods0.2870.0227.079
plot-DataGeNET.Psy-ANY-method0.0880.0050.094
plot-JaccardIndexPsy-ANY-method000
psygenetDisease-methods0.0430.0086.027
psygenetDiseaseSentences0.0280.0054.584
psygenetGene-methods0.0340.0054.182
psygenetGeneSentences 0.252 0.03537.159
qr0.0000.0010.000
topAnatEnrichment-methods000
universe0.0040.0000.004