* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/haploR.Rcheck’
* using R Under development (unstable) (2025-05-04 r88189)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-15 (GCC) 15.1.0
    GNU Fortran (GCC) 15.1.0
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘haploR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘haploR’ version ‘4.0.7’
* package encoding: UTF-8
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘haploR’ can be installed ... [10s/27s] 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 ... [3s/10s] OK
* checking use of S3 registration ... 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 ... [13s/38s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/71s] ERROR
Running examples in ‘haploR-Ex.R’ failed
The error most likely occurred in:

> ### Name: getExtendedView
> ### Title: This function queries HaploReg web-based tool in order to
> ###   Extended view for SNP of interest
> ### Aliases: getExtendedView
> 
> ### ** Examples
> 
> tables <- getExtendedView(snp="rs10048158")
Error in tables[[1]] : subscript out of bounds
Calls: getExtendedView
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [3s/132s]
 [3s/133s] ERROR
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
  > # Adapted from: http://rwiki.sciviews.org/doku.php?id=developers:runit
  > 
  > if( identical( .Platform$OS.type, "windows" ) && 
  +     identical( .Platform$r_arch, "x64" ) ){
  +   print( "unit tests not run on windows 64 (workaround alert)" )
  + } else {
  +   if(require("RUnit", quietly = TRUE)) {
  +     require("RCurl", quietly = TRUE)
  +     pkg <- "haploR"
  +     if(Sys.getenv("RCMDCHECK") == "FALSE") {
  +       path <- file.path(getwd(), "..", "inst", "unitTests")
  +     } else {
  +       path <- system.file(package=pkg, "unitTests")
  +     }
  + 
  +     cat("\nRunning unit tests:\n")
  +     print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
  +     
  +     library(package=pkg, character.only=TRUE)
  +     
  +     # Define tests
  +     testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), 
  +                                  dirs=path, 
  +                                  testFuncRegexp = "^test_+", 
  +                                  testFileRegexp = "^test_+")
  +     
  +     # Run
  +     tests <- runTestSuite(testSuite)
  +     
  +     # Default report name
  +     pathReport <- file.path(path, "report")
  +     
  +     # Report to stdout
  +     printTextProtocol(tests, showDetails=FALSE)
  +     
  +     # Return stop() to cause R CMD check stop in case of
  +     #  - failures i.e. FALSE to unit tests or
  +     #  - errors i.e. R errors
  +     tmp <- getErrors(tests)
  +     if(tmp$nFail > 0 | tmp$nErr > 0) {
  +       stop(paste("\n\nUnit testing failed (#test failures: ", tmp$nFail, ", 
  +                  #R errors: ",  tmp$nErr, ")\n\n", sep=""))
  +     }
  +     
  +   } else {
  +     print( "package RUnit not available, cannot run unit tests" )
  +   }       
  + }
  
  Running unit tests:
  $pkg
  [1] "haploR"
  
  $getwd
  [1] "/data/gannet/ripley/R/packages/tests-noLD/haploR.Rcheck/tests"
  
  $pathToUnitTests
  [1] "/data/gannet/ripley/R/packages/tests-noLD/haploR.Rcheck/haploR/unitTests"
  
  
  
  Executing test function test_queryHaploreg  ... Timing stopped at: 0.114 0.009 120.9
  Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed
  In addition: Warning messages:
  1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: Marsaglia-Multicarry has poor statistical properties
  2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
   done successfully.
  
  
  
  Executing test function test_queryRegulome  ... No encoding supplied: defaulting to UTF-8.
   done successfully.
  
  RUNIT TEST PROTOCOL -- Wed May  7 15:00:36 2025 
  *********************************************** 
  Number of test functions: 2 
  Number of errors: 1 
  Number of failures: 0 
  
   
  1 Test Suite : 
  haploR unit testing - 2 test functions, 1 error, 0 failures
  ERROR in test_queryHaploreg: Error in if (sp[[1]][i] != "") { : missing value where TRUE/FALSE needed
  Error: 
  
  Unit testing failed (#test failures: 0, 
                   #R errors: 1)
  
  In addition: Warning messages:
  1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: Marsaglia-Multicarry has poor statistical properties
  2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [18s/120s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘haplor-vignette.Rmd’ using rmarkdown

Quitting from haplor-vignette.Rmd:153-157 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (sp[[1]][i] != "") ...`:
! missing value where TRUE/FALSE needed
---
Backtrace:
    ▆
 1. └─haploR::queryHaploreg(query = c("rs10048158", "rs4791078"))
 2.   └─haploR:::simpleQuery(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'haplor-vignette.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘haplor-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘haplor-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [7s/19s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 3 ERRORs
See
  ‘/data/gannet/ripley/R/packages/tests-noLD/haploR.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 9:28.50, 96.38 + 12.64