##############################################################################
##############################################################################
###
### 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: getPages
> ### Title: Download SNPedia pages
> ### Aliases: getPages
> 
> ### ** Examples
> 
> res <- getPages(titles = "Rs1234")
> res
$Rs1234
[1] "{{Rsnum\n|rsid=1234\n|Gene=FAKE1\n|Chromosome=3\n|position=123615654\n|Orientation=plus\n|StabilizedOrientation=plus\n|Summary=a test snp 0.328905101289\n|geno1=(A;A)\n|geno2=(A;C)\n|geno3=(C;C)\n|Merged=1067\n|Status=Merged\n}}\n{{ population diversity\n|geno1=(A;A)\n|geno2=(A;C)\n|geno3=(C;C)\n|CEU |10 |60 |30\n|CHB |10.0 |10 |80\n|JPT |4.5 |20.5 |75.0\n|YRI |5.0 |33.3 |61.7\n|ASW |0 |0  |0\n|CHD |44.7 |43.5 |11.8\n|GIH |68.2 |28.4 |3.4\n|LWK |11.1 |25.6 |63.3\n|MEX |0.0 |0.0 |0.0\n|MKK |16.1 |42.7 |41.3\n|TSI |68.2 |27.1 |4.7\n|HapMapRevision=27\n}} This page represents an arbitrary [[SNP]]. The main text body of a SNP page summarizes the associations between SNP variants and a range of human traits (body height, disease risk, response to drugs, even behavior). The science that supports these associations (peer-reviewed publications with citations) is indicated by links to [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] abstracts in the form of <nowiki>{{PMID|12345678}}</nowiki> or [PMID 12345678] style citations.\n\nTechnically, there was once a valid rs1234, but it has long since been merged into a different identifier, due to the natural changes of that system. \n\nFor this reason, on SNPedia, we will use this SNP to explain how to use many key SNPedia features.\n\nTo the upper right you will see a box with these fields:\n\n*is a [[snp]] . This tells you that you are looking at a page about a snp. You may sometimes see the words [[gene]] or [[genotype]].\n*is mentioned by . This will show you what other pages on SNPedia are related to this snp.\n*dbSNP  rs1234 . This will take you to the the graphs of population diversity on its [http://www.ncbi.nlm.nih.gov/projects/SNP/ ncbi dbsnp] page.\n*hapmap rs1234. overlay snpedia on the [http://snpedia.blogspot.com/2007/12/gbrowse-snpedia.html hapmap] genome\n*ensembl rs1234 . Takes you to the snp report at [http://www.ensembl.org/info/about/index.html ensembl]\n*google . Automatic google search\n*23andMe . Links to the 23andMe.com web site where registered users can find their own genotypes for this SNP.\n*23andMe all. Links to the 23andMe.com web site where registered users can find discussions about this SNP.\n\nThe colored box indicates the frequency of each genotype in 4 [[HapMap]] populations. CEU is European so the box indicates that 10% of Europeans are (A;A) colored brown, 60% are (A;C) colored green, and 30% are (C;C) colored blue. The Chinese (CHB) and Japanese (JPT) are mainly (C;C).  Click on the question mark for [[help (population diversity)|more information]]."

> 
> res <- getPages(titles = c("Rs1234", "Rs1234(A;A)", "Rs1234(A;C)"))
Error: lexical error: invalid char in json text.
                                       <html> \n<head><title>502 Bad G
                     (right here) ------^
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
extractTags         0.277  0.022  17.288
getCategoryElements 0.149  0.007   7.860
* 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 1 | WARN 0 | SKIP 0 | PASS 2 ]
  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:49-53 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! lexical error: invalid char in json text.
                                       <html> \n<head><title>502 Bad G
                     (right here) ------^
---
Backtrace:
    ▆
 1. └─SNPediaR::getPages(titles = "Rs53576")
 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: 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-18.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── 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 1 | WARN 0 | SKIP 0 | PASS 2 ]
Error:
! Test failures.
Execution halted