CRAN Package Check Results for Package pcadapt

Last updated on 2020-01-27 00:48:10 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 4.1.0 96.58 102.96 199.54 WARN
r-devel-linux-x86_64-debian-gcc 4.1.0 65.55 81.78 147.33 OK
r-devel-linux-x86_64-fedora-clang 4.1.0 270.03 WARN
r-devel-linux-x86_64-fedora-gcc 4.1.0 249.41 OK
r-devel-windows-ix86+x86_64 4.1.0 173.00 7.00 180.00 ERROR
r-devel-windows-ix86+x86_64-gcc8 4.1.0 304.00 161.00 465.00 NOTE
r-patched-linux-x86_64 4.1.0 69.67 95.09 164.76 OK
r-patched-solaris-x86 4.1.0 280.00 NOTE
r-release-linux-x86_64 4.1.0 70.06 95.74 165.80 OK
r-release-windows-ix86+x86_64 4.1.0 185.00 139.00 324.00 NOTE
r-release-osx-x86_64 4.1.0 NOTE
r-oldrel-windows-ix86+x86_64 4.1.0 178.00 139.00 317.00 NOTE
r-oldrel-osx-x86_64 4.1.0 NOTE

Check Details

Version: 4.1.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'pcadapt.Rmd' using rmarkdown
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    pcadapt
     --- call from context ---
    read.pcadapt(genotypes, type = "pcadapt")
     --- call from argument ---
    if (class(input) == "character") {
     file2other(input, type, match.arg(type.out), match.arg(allele.sep))
    } else if (class(input) %in% c("matrix", "data.frame", "array")) {
     matrix2other(input, type)
    } else {
     stop("Input should be a file path or a matrix-like object.")
    }
     --- R stacktrace ---
    where 1: read.pcadapt(genotypes, type = "pcadapt")
    where 2: eval(expr, envir, enclos)
    where 3: eval(expr, envir, enclos)
    where 4: withVisible(eval(expr, envir, enclos))
    where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 9: evaluate::evaluate(...)
    where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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 11: 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$render, options)))
    where 12: block_exec(params)
    where 13: call_block(x)
    where 14: process_group.block(group)
    where 15: process_group(group)
    where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 17: process_file(text, output)
    where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     output_dir = getwd(), ...)
    where 20: vweave_rmarkdown(...)
    where 21: engine$weave(file, quiet = quiet, encoding = enc)
    where 22: doTryCatch(return(expr), name, parentenv, handler)
    where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 24: tryCatchList(expr, classes, parentenv, handlers)
    where 25: tryCatch({
     engine$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 26: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pcadapt.Rcheck/vign_test/pcadapt",
     ser_elibs = "/tmp/RtmpU4YfIX/file61e1693b07ea.rds")
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (input, type = c("pcadapt", "lfmm", "vcf", "bed", "ped",
     "pool", "example"), type.out = c("bed", "matrix"), allele.sep = c("/",
     "|"), pop.sizes, ploidy, local.env, blocksize)
    {
     if (!missing(local.env))
     warning("Argument 'local.env' is deprecated.")
     if (!missing(blocksize))
     warning("Argument 'blocksize' is deprecated.")
     if (!missing(pop.sizes))
     warning("Argument 'pop.sizes' is deprecated.")
     if (!missing(ploidy))
     warning("Argument 'ploidy' is deprecated.")
     type <- match.arg(type)
     if (class(input) == "character") {
     file2other(input, type, match.arg(type.out), match.arg(allele.sep))
     }
     else if (class(input) %in% c("matrix", "data.frame", "array")) {
     matrix2other(input, type)
     }
     else {
     stop("Input should be a file path or a matrix-like object.")
     }
    }
    <bytecode: 0x97fb808>
    <environment: namespace:pcadapt>
     --- function search by body ---
    Function read.pcadapt in namespace pcadapt has this body.
     ----------- END OF FAILURE REPORT --------------
    Quitting from lines 241-246 (pcadapt.Rmd)
    Error: processing vignette 'pcadapt.Rmd' failed with diagnostics:
    the condition has length > 1
    --- failed re-building 'pcadapt.Rmd'
    
    SUMMARY: processing the following file failed:
     'pcadapt.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 4.1.0
Check: package dependencies
Result: WARN
    Requires orphaned package: ‘robust’
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 4.1.0
Check: installed package size
Result: NOTE
     installed size is 8.3Mb
     sub-directories of 1Mb or more:
     doc 1.9Mb
     extdata 2.7Mb
     libs 2.9Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 4.1.0
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-devel-windows-ix86+x86_64