##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:psygenet2r.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings psygenet2r_1.37.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/psygenet2r.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘psygenet2r/DESCRIPTION’ ... OK
* this is package ‘psygenet2r’ version ‘1.37.1’
* checking package namespace information ... NOTE
Found export directives that require package ‘methods’:
  ‘exportClasses’ ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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   0.411  0.044  28.537
pantherGraphic-methods  0.342  0.055   6.607
enrichedPD-methods      0.098  0.004   6.259
psygenetDisease-methods 0.053  0.003   5.567
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─psygenet2r::psygenetDisease(...)
    7.   └─psygenet2r:::ListPsyGeNETIds(database, "disease")
    8.     └─psygenet2r:::download_data(oql)
    9.       └─base::tryCatch(...)
   10.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   11.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   12.             └─value[[3L]](cond)
   13.               └─base::rawToChar(...)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 17 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘case_study.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/psygenet2r.Rcheck/vign_test/psygenet2r/vignettes/case_study_files/figure-html/pubmed1-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/psygenet2r.Rcheck/vign_test/psygenet2r/vignettes/case_study_files/figure-html/gene-disease-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/psygenet2r.Rcheck/vign_test/psygenet2r/vignettes/case_study_files/figure-html/gene-psy-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/psygenet2r.Rcheck/vign_test/psygenet2r/vignettes/case_study_files/figure-html/panther-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/psygenet2r.Rcheck/vign_test/psygenet2r/vignettes/case_study_files/figure-html/gene-disease-2-1.png" but not available.

Quitting from lines 187-192 [sentences1_query] (case_study.Rmd)
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
argument 'x' must be a raw vector
--- failed re-building ‘case_study.Rmd’

--- re-building ‘general_overview.Rmd’ using rmarkdown

Quitting from lines 130-133 [search_gene_1] (general_overview.Rmd)
Error: processing vignette 'general_overview.Rmd' failed with diagnostics:
argument 'x' must be a raw vector
--- failed re-building ‘general_overview.Rmd’

SUMMARY: processing the following files failed:
  ‘case_study.Rmd’ ‘general_overview.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/psygenet2r.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL psygenet2r
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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
Warning in fun(libname, pkgname) :
  Package 'psygenet2r' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'psygenet2r' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package keeps a record of temporary installation path
* DONE (psygenet2r)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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)
Warning message:
In fun(libname, pkgname) :
  Package 'psygenet2r' is deprecated and will be removed from
  Bioconductor version 3.21
> 
> test_check("psygenet2r")
[ FAIL 1 | WARN 0 | SKIP 4 | PASS 17 ]

══ 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'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_basic_disease.R:38:3'): Query multiple and non existing disease into PsyGeNET ──
Error in `rawToChar(RCurl::getURL(url, readfunction = charToRaw(oql), upload = TRUE, 
    customrequest = "POST"))`: argument 'x' must be a raw vector
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test_basic_disease.R:38:3
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─psygenet2r::psygenetDisease(...)
  7.   └─psygenet2r:::ListPsyGeNETIds(database, "disease")
  8.     └─psygenet2r:::download_data(oql)
  9.       └─base::tryCatch(...)
 10.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.             └─value[[3L]](cond)
 13.               └─base::rawToChar(...)

[ FAIL 1 | WARN 0 | SKIP 4 | PASS 17 ]
Error: Test failures
Execution halted