CRAN Package Check Results for Package haploR

Last updated on 2019-03-14 00:46:39 CET.

Check Details

Version: 2.0.7
Check: tests
Result: ERROR
     Running ‘runTests.R’ [3s/13s]
    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)) {
     + 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] "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/haploR.Rcheck/tests"
    
     $pathToUnitTests
     [1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/haploR/unitTests"
    
    
    
     Executing test function test_LDlink.LDmatrix ... done successfully.
    
    
    
     Executing test function test_queryHaploreg ... done successfully.
    
    
    
     Executing test function test_queryRegulome ... Timing stopped at: 0.293 0.004 2.335
     Error in checkEqualsNumeric(dim(x$res.table)[1], 2) :
     Mean relative difference: 0.9974684
    
     done successfully.
    
     RUNIT TEST PROTOCOL -- Wed Mar 13 20:04:55 2019
     ***********************************************
     Number of test functions: 3
     Number of errors: 0
     Number of failures: 1
    
    
     1 Test Suite :
     haploR unit testing - 3 test functions, 0 errors, 1 failure
     FAILURE in test_queryRegulome: Error in checkEqualsNumeric(dim(x$res.table)[1], 2) :
     Mean relative difference: 0.9974684
    
     Error:
    
     Unit testing failed (#test failures: 1,
     #R errors: 0)
    
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.0.7
Check: examples
Result: ERROR
    Running examples in ‘haploR-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: queryHaploreg
    > ### Title: This function queries HaploReg web-based tool and returns
    > ### results.
    > ### Aliases: queryHaploreg
    >
    > ### ** Examples
    >
    > library(haploR)
    > data <- queryHaploreg(c("rs10048158","rs4791078"))
    <simpleError in curl::curl_fetch_memory(url, handle = handle): Timeout was reached: Resolving timed out after 10000 milliseconds>
    Error in `[.data.frame`(res.table, , i) : undefined columns selected
    Calls: queryHaploreg -> simpleQuery
    Execution halted
Flavor: r-patched-solaris-x86

Version: 2.0.7
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 335-344 (haplor-vignette.Rmd)
    Error: processing vignette 'haplor-vignette.Rmd' failed with diagnostics:
    there is no package called 'webshot'
    Execution halted
Flavor: r-patched-solaris-x86

Version: 2.0.7
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Quitting from lines 335-344 (haplor-vignette.Rmd)
    Error: processing vignette 'haplor-vignette.Rmd' failed with diagnostics:
    cannot open the connection
    Execution halted
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64