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CHECK report for psygenet2r on merida1

This page was generated on 2019-04-16 11:59:23 -0400 (Tue, 16 Apr 2019).

Package 1213/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psygenet2r 1.14.0
Alba Gutierrez-Sacristan
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/psygenet2r
Branch: RELEASE_3_8
Last Commit: ff765b2
Last Changed Date: 2018-10-30 11:42:00 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: psygenet2r
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:psygenet2r.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings psygenet2r_1.14.0.tar.gz
StartedAt: 2019-04-16 02:04:05 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:07:07 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 181.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: psygenet2r.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:psygenet2r.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings psygenet2r_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/psygenet2r.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psygenet2r/DESCRIPTION’ ... OK
* this is package ‘psygenet2r’ version ‘1.14.0’
* 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 ... WARNING
Found the following significant warnings:
  Note: possible error in 'psygenetGene(x, databse = "ALL")': unused argument (databse = "ALL") 
  Note: possible error in 'psygenetGene(x, databse = "ALL", ': unused argument (databse = "ALL") 
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/psygenet2r.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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: possible error in psygenetGene(x, databse = "ALL"):
  unused argument (databse = "ALL")
.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: possible error in psygenetGene(x, databse = "ALL"): unused
  argument (databse = "ALL")
.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: possible error in psygenetGene(x, databse = "ALL"): unused
  argument (databse = "ALL")
.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: possible error in psygenetGene(x, databse = "ALL", verbose =
  verbose): unused argument (databse = "ALL")
.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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
psygenetGeneSentences 0.375  0.032  16.714
* 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/psygenet2r.Rcheck/00check.log’
for details.



Installation output

psygenet2r.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL psygenet2r
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘psygenet2r’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'psygenetGene(x, databse = "ALL")': unused argument (databse = "ALL") 
Note: possible error in 'psygenetGene(x, databse = "ALL")': unused argument (databse = "ALL") 
Note: possible error in 'psygenetGene(x, databse = "ALL")': unused argument (databse = "ALL") 
Note: possible error in 'psygenetGene(x, databse = "ALL", ': unused argument (databse = "ALL") 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (psygenet2r)

Tests output

psygenet2r.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(psygenet2r)
> 
> test_check("psygenet2r")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 18 SKIPPED: 4 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  5.369   0.356  44.341 

Example timings

psygenet2r.Rcheck/psygenet2r-Ex.timings

nameusersystemelapsed
JaccardIndexPsy-class0.1210.0201.886
enrichedPD-methods0.1400.0133.335
extract0.0260.0070.032
extractSentences0.0050.0010.006
getUMLs-methods0.0450.0031.520
jaccardEstimation-methods0.1140.0091.722
ndisease0.0020.0020.003
ngene0.0020.0010.003
pantherGraphic-methods0.6640.0414.966
plot-DataGeNET.Psy-ANY-method0.0940.0020.097
plot-JaccardIndexPsy-ANY-method0.0000.0000.001
psygenetDisease-methods0.0800.0042.631
psygenetDiseaseSentences0.0460.0031.537
psygenetGene-methods0.0610.0042.099
psygenetGeneSentences 0.375 0.03216.714
qr0.0000.0010.000
topAnatEnrichment-methods0.0000.0000.001
universe0.0150.0000.015