CRAN Package Check Results for Package HWxtest

Last updated on 2020-01-11 13:47:24 CET.

Additional issues

gcc10

Check Details

Version: 1.1.9
Check: examples
Result: ERROR
    Running examples in 'HWxtest-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: hwx.test
    > ### Title: Test for HW by either full enumeration or Monte Carlo.
    > ### Aliases: hwx.test
    >
    > ### ** Examples
    >
    > # Data from Louis and Dempster 1987 Table 2 and Guo and Thompson 1992 Figure 2:
    > c <- c(0,3,1,5,18,1,3,7,5,2)
    > hwx.test(c)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    HWxtest
     --- call from context ---
    alleleCounts(c)
     --- call from argument ---
    if (class(gmat) != "matrix") gmat <- vec.to.matrix(gmat)
     --- R stacktrace ---
    where 1: alleleCounts(c)
    where 2: hwx.test.matrix(c, method = method, cutoff = cutoff, B = B, statName = statName,
     histobins = histobins, histobounds = histobounds, showCurve = showCurve,
     safeSecs = safeSecs, detail = detail)
    where 3: hwx.test(c, method = method, cutoff = cutoff, B = B, statName = statName,
     histobins = histobins, histobounds = histobounds, showCurve = showCurve,
     safeSecs = safeSecs, detail = detail)
    where 4: hwx.test.numeric(c)
    where 5: hwx.test(c)
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (gmat)
    {
     if (class(gmat) != "matrix")
     gmat <- vec.to.matrix(gmat)
     t <- fillUpper(gmat)
     k <- dim(t)[1]
     m <- integer(k)
     for (i in 1:k) {
     m[i] <- sum(t[i, ]) + t[i, i]
     }
     if (!is.null(rownames(gmat)))
     names(m) <- rownames(gmat)
     m
    }
    <bytecode: 0x1bf5668>
    <environment: namespace:HWxtest>
     --- function search by body ---
    Function alleleCounts in namespace HWxtest has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(gmat) != "matrix") gmat <- vec.to.matrix(gmat) :
     the condition has length > 1
    Calls: hwx.test ... hwx.test.numeric -> hwx.test -> hwx.test.matrix -> alleleCounts
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.1.9
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'HWxtest.Rmd' using rmarkdown
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    HWxtest
     --- call from context ---
    alleleCounts(c)
     --- call from argument ---
    if (class(gmat) != "matrix") gmat <- vec.to.matrix(gmat)
     --- R stacktrace ---
    where 1: alleleCounts(c)
    where 2: hwx.test.matrix(c, method = method, cutoff = cutoff, B = B, statName = statName,
     histobins = histobins, histobounds = histobounds, showCurve = showCurve,
     safeSecs = safeSecs, detail = detail)
    where 3: hwx.test(c, method = method, cutoff = cutoff, B = B, statName = statName,
     histobins = histobins, histobounds = histobounds, showCurve = showCurve,
     safeSecs = safeSecs, detail = detail)
    where 4: hwx.test.numeric(obs)
    where 5: hwx.test(obs)
    where 6: eval(expr, envir, enclos)
    where 7: eval(expr, envir, enclos)
    where 8: withVisible(eval(expr, envir, enclos))
    where 9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 10: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 12: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 13: evaluate::evaluate(...)
    where 14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
     options$include) 0L else 2L, output_handler = knit_handlers(options$render,
     options))
    where 15: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
     stop_on_error = if (options$error && options$include) 0L else 2L,
     output_handler = knit_handlers(options$render, options)))
    where 16: block_exec(params)
    where 17: call_block(x)
    where 18: process_group.block(group)
    where 19: process_group(group)
    where 20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 21: process_file(text, output)
    where 22: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    where 23: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     ...)
    where 24: vweave_rmarkdown(...)
    where 25: engine$weave(file, quiet = quiet, encoding = enc)
    where 26: doTryCatch(return(expr), name, parentenv, handler)
    where 27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 28: tryCatchList(expr, classes, parentenv, handlers)
    where 29: tryCatch({
     engine$weave(file, quiet = quiet, encoding = enc)
     setwd(startdir)
     output <- find_vignette_product(name, by = "weave", engine = engine)
     if (!have.makefile && vignette_is_tex(output)) {
     texi2pdf(file = output, clean = FALSE, quiet = quiet)
     output <- find_vignette_product(name, by = "texi2pdf",
     engine = engine)
     }
     outputs <- c(outputs, output)
    }, error = function(e) {
     thisOK <<- FALSE
     fails <<- c(fails, file)
     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
     file, conditionMessage(e)))
    })
    where 30: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/HWxtest.Rcheck/vign_test/HWxtest",
     ser_elibs = "/tmp/RtmpXv6dM1/file37df77c22098.rds")
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (gmat)
    {
     if (class(gmat) != "matrix")
     gmat <- vec.to.matrix(gmat)
     t <- fillUpper(gmat)
     k <- dim(t)[1]
     m <- integer(k)
     for (i in 1:k) {
     m[i] <- sum(t[i, ]) + t[i, i]
     }
     if (!is.null(rownames(gmat)))
     names(m) <- rownames(gmat)
     m
    }
    <bytecode: 0x9483c98>
    <environment: namespace:HWxtest>
     --- function search by body ---
    Function alleleCounts in namespace HWxtest has this body.
     ----------- END OF FAILURE REPORT --------------
    Quitting from lines 136-138 (HWxtest.Rmd)
    Error: processing vignette 'HWxtest.Rmd' failed with diagnostics:
    the condition has length > 1
    --- failed re-building 'HWxtest.Rmd'
    
    SUMMARY: processing the following file failed:
     'HWxtest.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.1.9
Check: compiled code
Result: NOTE
    File ‘HWxtest/libs/HWxtest.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc