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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SNPediaR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings SNPediaR_1.27.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/SNPediaR.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SNPediaR/DESCRIPTION' ... OK
* this is package 'SNPediaR' version '1.27.0'
* 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 '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 R 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 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"))
Error in function (type, msg, asError = TRUE)  : 
  schannel: CertGetCertificateChain trust error CERT_TRUST_IS_NOT_TIME_VALID
Calls: getPages -> getURL -> curlPerform -> <Anonymous> -> fun
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:
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(60L, "schannel: CertGetCertificateChain trust error CERT_TRUST_IS_NOT_TIME_VALID", 
      TRUE)`: schannel: CertGetCertificateChain trust error CERT_TRUST_IS_NOT_TIME_VALID
  Backtrace:
      ▆
   1. ├─SNPediaR::getCategoryElements(category = "Is_a_medical_condition") at tests.r:18:4
   2. │ └─RCurl::getURL(continueURL)
   3. │   └─RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   4. └─RCurl (local) `<fn>`(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  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: 2 ERRORs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/SNPediaR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL SNPediaR
###
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* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'SNPediaR' ...
** 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 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 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 (SNPediaR)
> 
> test_check ("SNPediaR")
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('tests.r:8:5'): get pages ────────────────────────────────────────────
<SSL_CACERT/GenericCurlError/error/condition>
Error in `function (type, msg, asError = TRUE) 
{
    if (!is.character(type)) {
        i = match(type, CURLcodeValues)
        typeName = if (is.na(i)) 
            character()
        else names(CURLcodeValues)[i]
    }
    typeName = gsub("^CURLE_", "", typeName)
    fun = (if (asError) 
        stop
    else warning)
    fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
        "GenericCurlError", "error", "condition")))
}(60L, "schannel: CertGetCertificateChain trust error CERT_TRUST_IS_NOT_TIME_VALID", 
    TRUE)`: schannel: CertGetCertificateChain trust error CERT_TRUST_IS_NOT_TIME_VALID
Backtrace:
    ▆
 1. ├─SNPediaR::getPages(titles = "Rs1234") at tests.r:8:4
 2. │ └─RCurl::getURL(pagesURL)
 3. │   └─RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
 4. └─RCurl (local) `<fn>`(...)
── Error ('tests.r:18:5'): get category elements ───────────────────────────────
<SSL_CACERT/GenericCurlError/error/condition>
Error in `function (type, msg, asError = TRUE) 
{
    if (!is.character(type)) {
        i = match(type, CURLcodeValues)
        typeName = if (is.na(i)) 
            character()
        else names(CURLcodeValues)[i]
    }
    typeName = gsub("^CURLE_", "", typeName)
    fun = (if (asError) 
        stop
    else warning)
    fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
        "GenericCurlError", "error", "condition")))
}(60L, "schannel: CertGetCertificateChain trust error CERT_TRUST_IS_NOT_TIME_VALID", 
    TRUE)`: schannel: CertGetCertificateChain trust error CERT_TRUST_IS_NOT_TIME_VALID
Backtrace:
    ▆
 1. ├─SNPediaR::getCategoryElements(category = "Is_a_medical_condition") at tests.r:18:4
 2. │ └─RCurl::getURL(continueURL)
 3. │   └─RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
 4. └─RCurl (local) `<fn>`(...)

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