Multiple platform build/check report for BioC 3.11 - CHECK report for psygenet2r on tokay2

Package: psygenet2r

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:psygenet2r.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings psygenet2r_1.20.0.tar.gz

StartedAt: 2020-09-28 05:24:27 -0400 (Mon, 28 Sep 2020)

EndedAt: 2020-09-28 05:28:15 -0400 (Mon, 28 Sep 2020)

EllapsedTime: 228.9 seconds

RetCode: 1

Status: ERROR

CheckDir: psygenet2r.Rcheck

Warnings: NA

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:psygenet2r.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings psygenet2r_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/psygenet2r.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.20.0'
* 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:
  Note: possible error in 'psygenetGene(x, databse = "ALL")': unused argument (databse = "ALL") 
  Note: possible error in 'psygenetGene(x, databse = "ALL", ': unused argument (databse = "ALL") 
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpUBAZdJ/R.INSTALLc98279f407/psygenet2r/man/topAnatEnrichment-methods.Rd:21: file link 'runTest' in package 'topGO' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-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
* 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 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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'psygenet2r-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: JaccardIndexPsy-class
> ### Title: Class JaccardIndexPsy
> ### Aliases: JaccardIndexPsy-class
> 
> ### ** Examples
> 
> ji <- jaccardEstimation( c( "COMT", "CLOCK", "DRD3" ), "umls:C0005586", "ALL" )
Error: Service Temporarily Unavailable
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'psygenet2r-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: JaccardIndexPsy-class
> ### Title: Class JaccardIndexPsy
> ### Aliases: JaccardIndexPsy-class
> 
> ### ** Examples
> 
> ji <- jaccardEstimation( c( "COMT", "CLOCK", "DRD3" ), "umls:C0005586", "ALL" )
Error: Service Temporarily Unavailable
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  [ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 16 ]
  1. Error: Test of object returned from 'psygenetDisease' is S4 and 'PsyGeNET.Psy' (@test_basic_disease.R#6) 
  2. Error: Query single and existing disease into PsyGeNET (@test_basic_disease.R#21) 
  3. Error: Query multiple and existing disease into PsyGeNET (@test_basic_disease.R#26) 
  4. Error: Query single and non existing disease into PsyGeNET (@test_basic_disease.R#31) 
  5. Error: Query multiple and non existing disease into PsyGeNET (@test_basic_disease.R#38) 
  6. Error: Query multiple and existing and non existing disease into PsyGeNET (@test_basic_disease.R#45) 
  7. Error: Query multiple, existing and duplicated disease into PsyGeNET (@test_basic_disease.R#52) 
  8. Error: Test of object returned from 'psygenetGene' is S4 and 'PsyGeNET.Psy' (@test_basic_gene.R#6) 
  9. Error: Query single and existing gene into PsyGeNET (@test_basic_gene.R#19) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  [ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 16 ]
  1. Error: Test of object returned from 'psygenetDisease' is S4 and 'PsyGeNET.Psy' (@test_basic_disease.R#6) 
  2. Error: Query single and existing disease into PsyGeNET (@test_basic_disease.R#21) 
  3. Error: Query multiple and existing disease into PsyGeNET (@test_basic_disease.R#26) 
  4. Error: Query single and non existing disease into PsyGeNET (@test_basic_disease.R#31) 
  5. Error: Query multiple and non existing disease into PsyGeNET (@test_basic_disease.R#38) 
  6. Error: Query multiple and existing and non existing disease into PsyGeNET (@test_basic_disease.R#45) 
  7. Error: Query multiple, existing and duplicated disease into PsyGeNET (@test_basic_disease.R#52) 
  8. Error: Test of object returned from 'psygenetGene' is S4 and 'PsyGeNET.Psy' (@test_basic_gene.R#6) 
  9. Error: Query single and existing gene into PsyGeNET (@test_basic_gene.R#19) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
* 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: 4 ERRORs, 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/psygenet2r.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/psygenet2r_1.20.0.tar.gz && rm -rf psygenet2r.buildbin-libdir && mkdir psygenet2r.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=psygenet2r.buildbin-libdir psygenet2r_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL psygenet2r_1.20.0.zip && rm psygenet2r_1.20.0.tar.gz psygenet2r_1.20.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  222k  100  222k    0     0  4465k      0 --:--:-- --:--:-- --:--:-- 5292k

install for i386

* installing *source* package 'psygenet2r' ...
** using staged installation
** 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
  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-3.11-bioc/tmpdir/RtmpUBAZdJ/R.INSTALLc98279f407/psygenet2r/man/topAnatEnrichment-methods.Rd:21: file link 'runTest' in package 'topGO' does not exist and so has been treated as a topic
    universe                                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

install for x64

* installing *source* package 'psygenet2r' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'psygenet2r' as psygenet2r_1.20.0.zip
* DONE (psygenet2r)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'psygenet2r' successfully unpacked and MD5 sums checked


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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")
-- 1. Error: Test of object returned from 'psygenetDisease' is S4 and 'PsyGeNET.
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetDisease(...)
  2. psygenet2r:::ListPsyGeNETIds(database, "disease")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

-- 2. Error: Query single and existing disease into PsyGeNET (@test_basic_diseas
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetDisease(...)
  2. psygenet2r:::ListPsyGeNETIds(database, "disease")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

-- 3. Error: Query multiple and existing disease into PsyGeNET (@test_basic_dise
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetDisease(...)
  2. psygenet2r:::ListPsyGeNETIds(database, "disease")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

-- 4. Error: Query single and non existing disease into PsyGeNET (@test_basic_di
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetDisease(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "disease")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 5. Error: Query multiple and non existing disease into PsyGeNET (@test_basic_
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetDisease(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "disease")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 6. Error: Query multiple and existing and non existing disease into PsyGeNET 
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetDisease(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "disease")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 7. Error: Query multiple, existing and duplicated disease into PsyGeNET (@tes
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetDisease(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "disease")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 8. Error: Test of object returned from 'psygenetGene' is S4 and 'PsyGeNET.Psy
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetGene(gene = "SLC6A4", database = "ALL", verbose = FALSE)
  2. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

-- 9. Error: Query single and existing gene into PsyGeNET (@test_basic_gene.R#19
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetGene(gene = "SLC6A4", database = "ALL", verbose = FALSE)
  2. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

-- 10. Error: Query multiple and existing genes into PsyGeNET (@test_basic_gene.
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetGene(...)
  2. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

-- 11. Error: Query single and non existing genes into PsyGeNET (@test_basic_gen
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetGene(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 12. Error: Query multiple and non existing genes into PsyGeNET (@test_basic_g
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetGene(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 13. Error: Query multiple and existing and non existing genes into PsyGeNET (
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetGene(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 14. Error: Query multiple, existing and duplicated genes into PsyGeNET (@test
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetGene(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 15. Error: Query existing Gene Id as character into PsyGeNET (@test_basic_gen
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetGene(gene = "4852", database = "ALL", verbose = FALSE)
  2. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

-- 16. Error: Query existing Gene Id as numeric into PsyGeNET (@test_basic_gene.
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetGene(gene = 4852, database = "ALL", verbose = FALSE)
  2. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 16 ]
1. Error: Test of object returned from 'psygenetDisease' is S4 and 'PsyGeNET.Psy' (@test_basic_disease.R#6) 
2. Error: Query single and existing disease into PsyGeNET (@test_basic_disease.R#21) 
3. Error: Query multiple and existing disease into PsyGeNET (@test_basic_disease.R#26) 
4. Error: Query single and non existing disease into PsyGeNET (@test_basic_disease.R#31) 
5. Error: Query multiple and non existing disease into PsyGeNET (@test_basic_disease.R#38) 
6. Error: Query multiple and existing and non existing disease into PsyGeNET (@test_basic_disease.R#45) 
7. Error: Query multiple, existing and duplicated disease into PsyGeNET (@test_basic_disease.R#52) 
8. Error: Test of object returned from 'psygenetGene' is S4 and 'PsyGeNET.Psy' (@test_basic_gene.R#6) 
9. Error: Query single and existing gene into PsyGeNET (@test_basic_gene.R#19) 
1. ...

Error: testthat unit tests failed
Execution halted


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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> library(testthat)
> library(psygenet2r)
> 
> test_check("psygenet2r")
-- 1. Error: Test of object returned from 'psygenetDisease' is S4 and 'PsyGeNET.
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetDisease(...)
  2. psygenet2r:::ListPsyGeNETIds(database, "disease")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

-- 2. Error: Query single and existing disease into PsyGeNET (@test_basic_diseas
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetDisease(...)
  2. psygenet2r:::ListPsyGeNETIds(database, "disease")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

-- 3. Error: Query multiple and existing disease into PsyGeNET (@test_basic_dise
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetDisease(...)
  2. psygenet2r:::ListPsyGeNETIds(database, "disease")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

-- 4. Error: Query single and non existing disease into PsyGeNET (@test_basic_di
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetDisease(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "disease")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 5. Error: Query multiple and non existing disease into PsyGeNET (@test_basic_
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetDisease(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "disease")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 6. Error: Query multiple and existing and non existing disease into PsyGeNET 
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetDisease(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "disease")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 7. Error: Query multiple, existing and duplicated disease into PsyGeNET (@tes
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetDisease(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "disease")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 8. Error: Test of object returned from 'psygenetGene' is S4 and 'PsyGeNET.Psy
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetGene(gene = "SLC6A4", database = "ALL", verbose = FALSE)
  2. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

-- 9. Error: Query single and existing gene into PsyGeNET (@test_basic_gene.R#19
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetGene(gene = "SLC6A4", database = "ALL", verbose = FALSE)
  2. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

-- 10. Error: Query multiple and existing genes into PsyGeNET (@test_basic_gene.
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetGene(...)
  2. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

-- 11. Error: Query single and non existing genes into PsyGeNET (@test_basic_gen
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetGene(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 12. Error: Query multiple and non existing genes into PsyGeNET (@test_basic_g
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetGene(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 13. Error: Query multiple and existing and non existing genes into PsyGeNET (
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetGene(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 14. Error: Query multiple, existing and duplicated genes into PsyGeNET (@test
Service Temporarily Unavailable
Backtrace:
  1. testthat::expect_warning(...)
  6. psygenet2r::psygenetGene(...)
  7. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  8. psygenet2r:::download_data(oql)
  9. base::tryCatch(...)
 10. base:::tryCatchList(expr, classes, parentenv, handlers)
 11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. value[[3L]](cond)
 14. RCurl::getURLContent(...)
 15. RCurl:::stop.if.HTTP.error(http.header)

-- 15. Error: Query existing Gene Id as character into PsyGeNET (@test_basic_gen
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetGene(gene = "4852", database = "ALL", verbose = FALSE)
  2. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

-- 16. Error: Query existing Gene Id as numeric into PsyGeNET (@test_basic_gene.
Service Temporarily Unavailable
Backtrace:
  1. psygenet2r::psygenetGene(gene = 4852, database = "ALL", verbose = FALSE)
  2. psygenet2r:::ListPsyGeNETIds(database, "Gene")
  3. psygenet2r:::download_data(oql)
  4. base::tryCatch(...)
  5. base:::tryCatchList(expr, classes, parentenv, handlers)
  6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[[3L]](cond)
  9. RCurl::getURLContent(...)
 10. RCurl:::stop.if.HTTP.error(http.header)

== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 16 ]
1. Error: Test of object returned from 'psygenetDisease' is S4 and 'PsyGeNET.Psy' (@test_basic_disease.R#6) 
2. Error: Query single and existing disease into PsyGeNET (@test_basic_disease.R#21) 
3. Error: Query multiple and existing disease into PsyGeNET (@test_basic_disease.R#26) 
4. Error: Query single and non existing disease into PsyGeNET (@test_basic_disease.R#31) 
5. Error: Query multiple and non existing disease into PsyGeNET (@test_basic_disease.R#38) 
6. Error: Query multiple and existing and non existing disease into PsyGeNET (@test_basic_disease.R#45) 
7. Error: Query multiple, existing and duplicated disease into PsyGeNET (@test_basic_disease.R#52) 
8. Error: Test of object returned from 'psygenetGene' is S4 and 'PsyGeNET.Psy' (@test_basic_gene.R#6) 
9. Error: Query single and existing gene into PsyGeNET (@test_basic_gene.R#19) 
1. ...

Error: testthat unit tests failed
Execution halted

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CHECK report for psygenet2r on tokay2

Summary

Command output

Installation output

Tests output

Example timings