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CHECK report for psygenet2r on tokay1

This page was generated on 2018-04-12 13:27:39 -0400 (Thu, 12 Apr 2018).

Package 1086/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psygenet2r 1.10.0
Alba Gutierrez-Sacristan
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/psygenet2r
Branch: RELEASE_3_6
Last Commit: 12d5d24
Last Changed Date: 2017-10-30 12:41:14 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: psygenet2r
Version: 1.10.0
Command: rm -rf psygenet2r.buildbin-libdir psygenet2r.Rcheck && mkdir psygenet2r.buildbin-libdir psygenet2r.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=psygenet2r.buildbin-libdir psygenet2r_1.10.0.tar.gz >psygenet2r.Rcheck\00install.out 2>&1 && cp psygenet2r.Rcheck\00install.out psygenet2r-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=psygenet2r.buildbin-libdir --install="check:psygenet2r-install.out" --force-multiarch --no-vignettes --timings psygenet2r_1.10.0.tar.gz
StartedAt: 2018-04-12 02:19:15 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:23:38 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 262.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: psygenet2r.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf psygenet2r.buildbin-libdir psygenet2r.Rcheck && mkdir psygenet2r.buildbin-libdir psygenet2r.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=psygenet2r.buildbin-libdir psygenet2r_1.10.0.tar.gz >psygenet2r.Rcheck\00install.out 2>&1 && cp psygenet2r.Rcheck\00install.out psygenet2r-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=psygenet2r.buildbin-libdir --install="check:psygenet2r-install.out" --force-multiarch --no-vignettes --timings psygenet2r_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/psygenet2r.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'psygenet2r/DESCRIPTION' ... OK
* this is package 'psygenet2r' version '1.10.0'
* 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 whether package 'psygenet2r' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpY1iBeT/R.INSTALL137055115d8f/psygenet2r/man/topAnatEnrichment-methods.Rd:21: missing file link 'runTest'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/psygenet2r.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 global function definition for 'data'
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 data 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", "data", "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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
psygenetGeneSentences 0.26   0.06   12.25
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
psygenetGeneSentences 0.16   0.02   12.28
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/psygenet2r.Rcheck/00check.log'
for details.



Installation output

psygenet2r.Rcheck/00install.out


install for i386

* installing *source* package 'psygenet2r' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'psygenet2r'
    finding HTML links ... done
    DataGeNET.Psy-class                     html  
    JaccardIndexPsy-class                   html  
    enrichedPD-methods                      html  
    extract                                 html  
    extractSentences                        html  
    geneAttrPlot-methods                    html  
    getUMLs-methods                         html  
    jaccardEstimation-methods               html  
    ndisease                                html  
    ngene                                   html  
    pantherGraphic-methods                  html  
    plot-DataGeNET.Psy-ANY-method           html  
    plot-JaccardIndexPsy-ANY-method         html  
    psygenet2r                              html  
    psygenetDisease-methods                 html  
    psygenetDiseaseSentences                html  
    psygenetGene-methods                    html  
    psygenetGeneSentences                   html  
    qr                                      html  
    topAnatEnrichment-methods               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpY1iBeT/R.INSTALL137055115d8f/psygenet2r/man/topAnatEnrichment-methods.Rd:21: missing file link 'runTest'
    universe                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'psygenet2r' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'psygenet2r' as psygenet2r_1.10.0.zip
* DONE (psygenet2r)
In R CMD INSTALL
In R CMD INSTALL

Tests output

psygenet2r.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   4.50    0.31   38.14 

psygenet2r.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(psygenet2r)
> 
> test_check("psygenet2r")
== testthat results  ===========================================================
OK: 18 SKIPPED: 4 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   6.28    0.25   38.46 

Example timings

psygenet2r.Rcheck/examples_i386/psygenet2r-Ex.timings

nameusersystemelapsed
JaccardIndexPsy-class0.250.001.64
enrichedPD-methods0.370.003.12
extract0.000.020.02
extractSentences000
getUMLs-methods0.020.001.26
jaccardEstimation-methods0.050.011.50
ndisease0.010.000.02
ngene000
pantherGraphic-methods0.440.024.06
plot-DataGeNET.Psy-ANY-method0.70.00.7
plot-JaccardIndexPsy-ANY-method000
psygenetDisease-methods0.080.002.30
psygenetDiseaseSentences0.030.001.27
psygenetGene-methods0.070.001.76
psygenetGeneSentences 0.26 0.0612.25
qr000
topAnatEnrichment-methods000
universe0.220.000.22

psygenet2r.Rcheck/examples_x64/psygenet2r-Ex.timings

nameusersystemelapsed
JaccardIndexPsy-class0.240.011.65
enrichedPD-methods0.220.022.88
extract000
extractSentences000
getUMLs-methods0.190.001.43
jaccardEstimation-methods0.090.001.41
ndisease000
ngene000
pantherGraphic-methods0.570.004.22
plot-DataGeNET.Psy-ANY-method1.030.011.04
plot-JaccardIndexPsy-ANY-method000
psygenetDisease-methods0.030.022.30
psygenetDiseaseSentences0.050.011.30
psygenetGene-methods0.150.021.84
psygenetGeneSentences 0.16 0.0212.28
qr000
topAnatEnrichment-methods000
universe000