CRAN Package Check Results for Package iNEXT

Last updated on 2020-01-11 09:49:08 CET.

Check Details

Version: 2.0.19
Check: examples
Result: ERROR
    Running examples in 'iNEXT-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: as.abucount
    > ### Title: Transform abundance raw data to abundance row-sum counts (iNEXT
    > ### input format)
    > ### Aliases: as.abucount
    >
    > ### ** Examples
    >
    > data(ciliates)
    > lapply(ciliates, as.abucount)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    iNEXT
     --- call from context ---
    FUN(X[[i]], ...)
     --- call from argument ---
    if (class(x) == "data.frame" | class(x) == "matrix") {
     y <- rowSums(x)
     y
    } else if (class(x) == "numeric" | class(x) == "integer" | class(x) ==
     "double") {
     warnings("Ambiguous data type, the input object is a vector. Set total number of sampling units as 1.")
     x
    } else {
     stop("invalid data type, it should be a data.frame or matrix.")
    }
     --- R stacktrace ---
    where 1: FUN(X[[i]], ...)
    where 2: lapply(ciliates, as.abucount)
    
     --- value of length: 2 type: logical ---
    [1] TRUE FALSE
     --- function from context ---
    function (x)
    {
     if (class(x) == "data.frame" | class(x) == "matrix") {
     y <- rowSums(x)
     y
     }
     else if (class(x) == "numeric" | class(x) == "integer" |
     class(x) == "double") {
     warnings("Ambiguous data type, the input object is a vector. Set total number of sampling units as 1.")
     x
     }
     else {
     stop("invalid data type, it should be a data.frame or matrix.")
     }
    }
    <bytecode: 0x4770be0>
    <environment: namespace:iNEXT>
     --- function search by body ---
    Function as.abucount in namespace iNEXT has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(x) == "data.frame" | class(x) == "matrix") { :
     the condition has length > 1
    Calls: lapply -> FUN
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.0.19
Check: tests
Result: ERROR
     Running 'testthat.R' [11s/12s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(iNEXT)
     >
     > test_check("iNEXT")
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     iNEXT
     --- call from context ---
     FUN(X[[i]], ...)
     --- call from argument ---
     if (class(x) == "data.frame" | class(x) == "matrix") {
     a <- sort(as.numeric(unique(c(unlist(x)))))
     if (!identical(a, c(0, 1))) {
     warning("Invalid data type, the element of species by sites presence-absence matrix should be 0 or 1. Set nonzero elements as 1.")
     x <- (x > 0)
     }
     nT <- ncol(x)
     y <- rowSums(x)
     y <- c(nT, y)
     y
     } else if (class(x) == "numeric" | class(x) == "integer" | class(x) ==
     "double") {
     warnings("Ambiguous data type, the input object is a vector. Set total number of sampling units as 1.")
     c(1, x)
     } else {
     stop("Invalid data type, it should be a data.frame or matrix.")
     }
     --- R stacktrace ---
     where 1: FUN(X[[i]], ...)
     where 2: lapply(x, as.incfreq)
     where 3 at testthat/test-iNEXT.R#51: iNEXT(ciliates, q = 0, datatype = "incidence_raw")
     where 4: eval(code, test_env)
     where 5: eval(code, test_env)
     where 6: withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error)
     where 7: doTryCatch(return(expr), name, parentenv, handler)
     where 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 9: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 10: doTryCatch(return(expr), name, parentenv, handler)
     where 11: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 12: tryCatchList(expr, classes, parentenv, handlers)
     where 13: tryCatch(withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error), error = handle_fatal,
     skip = function(e) {
     })
     where 14: test_code(desc, code, env = parent.frame())
     where 15 at testthat/test-iNEXT.R#47: test_that("iNEXT for species by sampling-units incidence matrix",
     {
     data(ciliates)
     options(warn = -1)
     out <- iNEXT(ciliates, q = 0, datatype = "incidence_raw")
     expect_is(out, "iNEXT")
     expect_output(str(out), "List of 3")
     expect_equal(names(out$DataInfo)[2], "T")
     expect_equal(nrow(out$DataInfo), length(ciliates))
     x <- ciliates$EtoshaPan
     expect_equal(class(x), "matrix")
     out <- iNEXT(x, q = 0, datatype = "incidence_raw")
     expect_is(out, "iNEXT")
     expect_output(str(out), "List of 3")
     expect_equal(names(out$DataInfo)[2], "T")
     expect_equal(nrow(out$DataInfo), 1)
     })
     where 16: eval(code, test_env)
     where 17: eval(code, test_env)
     where 18: withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error)
     where 19: doTryCatch(return(expr), name, parentenv, handler)
     where 20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 21: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 22: doTryCatch(return(expr), name, parentenv, handler)
     where 23: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 24: tryCatchList(expr, classes, parentenv, handlers)
     where 25: tryCatch(withCallingHandlers({
     eval(code, test_env)
     if (!handled && !is.null(test)) {
     skip_empty()
     }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
     message = handle_message, error = handle_error), error = handle_fatal,
     skip = function(e) {
     })
     where 26: test_code(NULL, exprs, env)
     where 27: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     where 28: force(code)
     where 29: doWithOneRestart(return(expr), restart)
     where 30: withOneRestart(expr, restarts[[1L]])
     where 31: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 32: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
     {
     reporter$start_file(basename(path))
     lister$start_file(basename(path))
     source_file(path, new.env(parent = env), chdir = TRUE,
     wrap = wrap)
     reporter$.end_context()
     reporter$end_file()
     })
     where 33: FUN(X[[i]], ...)
     where 34: lapply(paths, test_file, env = env, reporter = current_reporter,
     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     where 35: force(code)
     where 36: doWithOneRestart(return(expr), restart)
     where 37: withOneRestart(expr, restarts[[1L]])
     where 38: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 39: with_reporter(reporter = current_reporter, results <- lapply(paths,
     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
     load_helpers = FALSE, wrap = wrap))
     where 40: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 41: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
     wrap = wrap)
     where 42: test_package_dir(package = package, test_path = test_path, filter = filter,
     reporter = reporter, ..., stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 43: test_check("iNEXT")
    
     --- value of length: 2 type: logical ---
     [1] TRUE FALSE
     --- function from context ---
     function (x)
     {
     if (class(x) == "data.frame" | class(x) == "matrix") {
     a <- sort(as.numeric(unique(c(unlist(x)))))
     if (!identical(a, c(0, 1))) {
     warning("Invalid data type, the element of species by sites presence-absence matrix should be 0 or 1. Set nonzero elements as 1.")
     x <- (x > 0)
     }
     nT <- ncol(x)
     y <- rowSums(x)
     y <- c(nT, y)
     y
     }
     else if (class(x) == "numeric" | class(x) == "integer" |
     class(x) == "double") {
     warnings("Ambiguous data type, the input object is a vector. Set total number of sampling units as 1.")
     c(1, x)
     }
     else {
     stop("Invalid data type, it should be a data.frame or matrix.")
     }
     }
     <bytecode: 0x2f2c848>
     <environment: namespace:iNEXT>
     --- function search by body ---
     Function as.incfreq in namespace iNEXT has this body.
     ----------- END OF FAILURE REPORT --------------
     -- 1. Error: iNEXT for species by sampling-units incidence matrix (@test-iNEXT.R
     the condition has length > 1
     Backtrace:
     1. iNEXT::iNEXT(ciliates, q = 0, datatype = "incidence_raw")
     2. base::lapply(x, as.incfreq)
     3. iNEXT:::FUN(X[[i]], ...)
    
     == testthat results ===========================================================
     [ OK: 20 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
     1. Error: iNEXT for species by sampling-units incidence matrix (@test-iNEXT.R#51)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.0.19
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'Introduction.Rmd' using rmarkdown
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    iNEXT
     --- call from context ---
    FUN(X[[i]], ...)
     --- call from argument ---
    if (class(x) == "data.frame" | class(x) == "matrix") {
     a <- sort(as.numeric(unique(c(unlist(x)))))
     if (!identical(a, c(0, 1))) {
     warning("Invalid data type, the element of species by sites presence-absence matrix should be 0 or 1. Set nonzero elements as 1.")
     x <- (x > 0)
     }
     nT <- ncol(x)
     y <- rowSums(x)
     y <- c(nT, y)
     y
    } else if (class(x) == "numeric" | class(x) == "integer" | class(x) ==
     "double") {
     warnings("Ambiguous data type, the input object is a vector. Set total number of sampling units as 1.")
     c(1, x)
    } else {
     stop("Invalid data type, it should be a data.frame or matrix.")
    }
     --- R stacktrace ---
    where 1: FUN(X[[i]], ...)
    where 2: lapply(x, as.incfreq)
    where 3: iNEXT(ciliates, datatype = "incidence_raw", endpoint = 150)
    where 4: eval(expr, envir, enclos)
    where 5: eval(expr, envir, enclos)
    where 6: withVisible(eval(expr, envir, enclos))
    where 7: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 8: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 11: evaluate::evaluate(...)
    where 12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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 13: 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$render, options)))
    where 14: block_exec(params)
    where 15: call_block(x)
    where 16: process_group.block(group)
    where 17: process_group(group)
    where 18: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 19: process_file(text, output)
    where 20: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    where 21: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     ...)
    where 22: vweave_rmarkdown(...)
    where 23: engine$weave(file, quiet = quiet, encoding = enc)
    where 24: doTryCatch(return(expr), name, parentenv, handler)
    where 25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 26: tryCatchList(expr, classes, parentenv, handlers)
    where 27: tryCatch({
     engine$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 28: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/iNEXT.Rcheck/vign_test/iNEXT",
     ser_elibs = "/tmp/RtmpyiW9Ma/file22757dd2f9ff.rds")
    
     --- value of length: 2 type: logical ---
    [1] TRUE FALSE
     --- function from context ---
    function (x)
    {
     if (class(x) == "data.frame" | class(x) == "matrix") {
     a <- sort(as.numeric(unique(c(unlist(x)))))
     if (!identical(a, c(0, 1))) {
     warning("Invalid data type, the element of species by sites presence-absence matrix should be 0 or 1. Set nonzero elements as 1.")
     x <- (x > 0)
     }
     nT <- ncol(x)
     y <- rowSums(x)
     y <- c(nT, y)
     y
     }
     else if (class(x) == "numeric" | class(x) == "integer" |
     class(x) == "double") {
     warnings("Ambiguous data type, the input object is a vector. Set total number of sampling units as 1.")
     c(1, x)
     }
     else {
     stop("Invalid data type, it should be a data.frame or matrix.")
     }
    }
    <bytecode: 0x8dfe598>
    <environment: namespace:iNEXT>
     --- function search by body ---
     ----------- END OF FAILURE REPORT --------------
    Quitting from lines 355-357 (Introduction.Rmd)
    Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
    the condition has length > 1
    --- failed re-building 'Introduction.Rmd'
    
    SUMMARY: processing the following file failed:
     'Introduction.Rmd'
    
    Error: Vignette re-building failed.
    In addition: Warning messages:
    1: Removed 15 rows containing missing values (geom_path).
    2: Removed 15 rows containing missing values (geom_path).
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.0.19
Check: tests
Result: ERROR
     Running ‘testthat.R’ [9s/13s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(iNEXT)
     >
     > test_check("iNEXT")
     ── 1. Failure: iNEXT for species by sampling-units incidence matrix (@test-iNEXT
     class(x) not equal to "matrix".
     Lengths differ: 2 is not 1
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 28 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
     1. Failure: iNEXT for species by sampling-units incidence matrix (@test-iNEXT.R#59)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc