##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SNPediaR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SNPediaR_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SNPediaR.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SNPediaR/DESCRIPTION’ ... OK
* this is package ‘SNPediaR’ version ‘1.36.0’
* 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 ‘SNPediaR’ 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 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘SNPediaR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: extractTags
> ### Title: Extract information form downloaded SNPedia pages.
> ### Aliases: extractTags extractSnpTags extractGenotypeTags
> 
> ### ** Examples
> 
> res <- getPages (c ("Rs1234", "Rs53576"))
> t (sapply (res, extractSnpTags))
        rsid    Chromosome position    Orientation GMAF     Assembly
Rs1234  "1234"  "3"        "123615654" "plus"      NA       NA      
Rs53576 "53576" "3"        "8762685"   "plus"      "0.4128" "GRCh38"
        GenomeBuild dbSNPBuild geno1   geno2   geno3   StabilizedOrientation
Rs1234  NA          NA         "(A;A)" "(A;C)" "(C;C)" "plus"               
Rs53576 "38.1"      "141"      "(A;A)" "(A;G)" "(G;G)" "plus"               
        Status   Merged Gene    Gene_s
Rs1234  "Merged" "1067" "FAKE1" NA    
Rs53576 NA       NA     "OXTR"  "OXTR"
        Summary                                     
Rs1234  "a test snp 0.328905101289"                 
Rs53576 "influences social behavior and personality"
> 
> extractTags (res[[1]], tags = c("rsid", "Chromosome", "position"))
       rsid  Chromosome    position 
     "1234"         "3" "123615654" 
> 
> res <- getPages (c ("Rs1234(A;A)", "Rs1234(A;C)","Rs1234(C;C)"))
> t (sapply (res, extractGenotypeTags))
            rsid   allele1 allele2 repute magnitude
Rs1234(A;A) "1234" "A"     "A"     "Bad"  "2"      
Rs1234(A;C) "1234" "A"     "C"     "Good" "1.5"    
Rs1234(C;C) "1234" "C"     "C"     NA     "0"      
            summary                          
Rs1234(A;A) "summary of something bad"       
Rs1234(A;C) "heterozygote for something good"
Rs1234(C;C) "normal"                         
> 
> getPages (c ("Rs1234(A;A)", "Rs1234(A;C)","Rs1234(C;C)"),
+           wikiParseFunction = extractGenotypeTags)
$`Rs1234(A;A)`
                      rsid                    allele1 
                    "1234"                        "A" 
                   allele2                     repute 
                       "A"                      "Bad" 
                 magnitude                    summary 
                       "2" "summary of something bad" 

$`Rs1234(A;C)`
                             rsid                           allele1 
                           "1234"                               "A" 
                          allele2                            repute 
                              "C"                            "Good" 
                        magnitude                           summary 
                            "1.5" "heterozygote for something good" 

$`Rs1234(C;C)`
     rsid   allele1   allele2    repute magnitude   summary 
   "1234"       "C"       "C"        NA       "0"  "normal" 

> 
> getPages (c ("Rs1234(A;A)", "Rs1234(A;C)","Rs1234(C;C)"),
+           wikiParseFunction = extractGenotypeTags,
+           tags = c("rsid", "allele1", "allele2"))
Error: lexical error: invalid char in json text.
                                       <html> \n<head><title>502 Bad G
                     (right here) ------^
Execution halted
* 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:
                                         <html> \n<head><title>502 Bad G
                       (right here) ------^
  
  Backtrace:
      ▆
   1. └─SNPediaR::getCategoryElements(category = "Is_a_medical_condition") at tests.r:18:5
   2.   └─jsonlite::fromJSON(lineas)
   3.     └─jsonlite:::parse_and_simplify(...)
   4.       └─jsonlite:::parseJSON(txt, bigint_as_char)
   5.         └─jsonlite:::parse_string(txt, bigint_as_char)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
  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 ‘SNPediaR.Rmd’ using rmarkdown

Quitting from SNPediaR.Rmd:148-151 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! lexical error: invalid char in json text.
                                       <html> \n<head><title>502 Bad G
                     (right here) ------^
---
Backtrace:
    ▆
 1. └─SNPediaR::getCategoryElements(category = "Is_a_medical_condition")
 2.   └─jsonlite::fromJSON(lineas)
 3.     └─jsonlite:::parse_and_simplify(...)
 4.       └─jsonlite:::parseJSON(txt, bigint_as_char)
 5.         └─jsonlite:::parse_string(txt, bigint_as_char)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SNPediaR.Rmd' failed with diagnostics:
lexical error: invalid char in json text.
                                       <html> \n<head><title>502 Bad G
                     (right here) ------^

--- failed re-building ‘SNPediaR.Rmd’

SUMMARY: processing the following file failed:
  ‘SNPediaR.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SNPediaR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SNPediaR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SNPediaR’ ...
** this is package ‘SNPediaR’ version ‘1.36.0’
** using staged installation
** R
** 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 (SNPediaR)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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 (SNPediaR)
> 
> test_check ("SNPediaR")
Saving _problems/tests-8.R
Saving _problems/tests-18.R
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('tests.r:8:5'): get pages ────────────────────────────────────────────
Error: lexical error: invalid char in json text.
                                       <html> \n<head><title>502 Bad G
                     (right here) ------^

Backtrace:
    ▆
 1. └─SNPediaR::getPages(titles = "Rs1234") at tests.r:8:5
 2.   └─jsonlite::fromJSON(datos)
 3.     └─jsonlite:::parse_and_simplify(...)
 4.       └─jsonlite:::parseJSON(txt, bigint_as_char)
 5.         └─jsonlite:::parse_string(txt, bigint_as_char)
── Error ('tests.r:18:5'): get category elements ───────────────────────────────
Error: lexical error: invalid char in json text.
                                       <html> \n<head><title>502 Bad G
                     (right here) ------^

Backtrace:
    ▆
 1. └─SNPediaR::getCategoryElements(category = "Is_a_medical_condition") at tests.r:18:5
 2.   └─jsonlite::fromJSON(lineas)
 3.     └─jsonlite:::parse_and_simplify(...)
 4.       └─jsonlite:::parseJSON(txt, bigint_as_char)
 5.         └─jsonlite:::parse_string(txt, bigint_as_char)

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
Error:
! Test failures.
Execution halted