CRAN Package Check Results for Package iNextPD

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

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3.2 7.68 83.79 91.47 ERROR
r-devel-linux-x86_64-debian-gcc 0.3.2 6.29 90.93 97.22 OK
r-devel-linux-x86_64-fedora-clang 0.3.2 158.44 OK
r-devel-linux-x86_64-fedora-gcc 0.3.2 150.21 OK
r-devel-windows-ix86+x86_64 0.3.2 28.00 136.00 164.00 OK
r-devel-windows-ix86+x86_64-gcc8 0.3.2 21.00 203.00 224.00 OK
r-patched-linux-x86_64 0.3.2 6.63 110.94 117.57 OK
r-patched-solaris-x86 0.3.2 219.10 OK
r-release-linux-x86_64 0.3.2 6.60 108.46 115.06 OK
r-release-windows-ix86+x86_64 0.3.2 21.00 183.00 204.00 OK
r-release-osx-x86_64 0.3.2 OK
r-oldrel-windows-ix86+x86_64 0.3.2 10.00 145.00 155.00 OK
r-oldrel-osx-x86_64 0.3.2 OK

Check Details

Version: 0.3.2
Check: examples
Result: ERROR
    Running examples in 'iNextPD-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: SPBoot
    > ### Title: Estimation of species relative abundance or detection
    > ### probability distribution
    > ### Aliases: SPBoot
    >
    > ### ** Examples
    >
    > data(bird)
    > bird.inc <- bird$inci
    > SPBoot(bird$abun, datatype="abundance")
    $North.site
     Acanthiza_pusilla Rhipidura_albicollis
     0.202970297 0.089108910
     Pachycephala_pectoralis Zosterops_lateralis
     0.079207914 0.079207914
     Pardalotus_punctatus Gerygone_mouki
     0.074257406 0.059405543
     Cormobates_leucophaea Meliphaga_lewinii
     0.054454394 0.054454394
     Menura_novaehollandiae Rhipidura_rufifrons
     0.044547402 0.039586152
     Psophodes_olivaceus Cacomantis_flabelliformis
     0.034609444 0.024505461
     Eopsaltria_australis Calyptorhynchus_funereus
     0.024505461 0.019252435
     Colluricincla_harmonica Alisterus_scapularis
     0.019252435 0.013711189
     Strepera_graculina Dacelo_novaeguineae
     0.013711189 0.007808497
     Platycercus_elegans Ptilonorhynchus_violaceus
     0.007808497 0.007808497
     Sericornis_frontalis
     0.007808497 0.005901447
    
     0.005901447 0.005901447
    
     0.005901447 0.005901447
     Cacatua_galerita Corvus_coronoides
     0.002085140 0.002085140
     Leucosarcia_melanoleuca Monarcha_melanopsis
     0.002085140 0.002085140
     Oriolus_sagittatus Petroica_rosea
     0.002085140 0.002085140
     Acanthiza_lineata Acanthiza_nana
     0.000000000 0.000000000
    Acanthorhynchus_tenuirostris Lichenostomus_chrysops
     0.000000000 0.000000000
     Malurus_cyaneus Malurus_lamberti
     0.000000000 0.000000000
     Manorina_melanophrys Neochmia_temporalis
     0.000000000 0.000000000
     Pachycephala_olivacea Pachycephala_rufiventris
     0.000000000 0.000000000
     Phylidonyris_niger Ptiloris_paradiseus
     0.000000000 0.000000000
     Sericornis_citreogularis Zoothera_lunulata
     0.000000000 0.000000000
    
    $South.site
     Cormobates_leucophaea Acanthiza_pusilla
     0.104234528 0.100977199
     Rhipidura_albicollis Acanthiza_nana
     0.065146580 0.058631921
     Meliphaga_lewinii Pardalotus_punctatus
     0.058631921 0.055374591
     Zosterops_lateralis Pachycephala_pectoralis
     0.055374591 0.048859923
     Rhipidura_rufifrons Gerygone_mouki
     0.045602574 0.032571812
     Monarcha_melanopsis Manorina_melanophrys
     0.032571812 0.029312227
     Neochmia_temporalis Platycercus_elegans
     0.029312227 0.022778664
     Psophodes_olivaceus Colluricincla_harmonica
     0.022778664 0.019490072
     Malurus_cyaneus Malurus_lamberti
     0.019490072 0.019490072
     Sericornis_frontalis Cacomantis_flabelliformis
     0.019490072 0.016162296
     Eopsaltria_australis Menura_novaehollandiae
     0.016162296 0.016162296
     Lichenostomus_chrysops Strepera_graculina
     0.012754851 0.012754851
     Acanthiza_lineata Pachycephala_rufiventris
     0.009205941 0.009205941
     Ptiloris_paradiseus Acanthorhynchus_tenuirostris
     0.009205941 0.005480418
     Cacatua_galerita Pachycephala_olivacea
     0.005480418 0.005480418
     Phylidonyris_niger Ptilonorhynchus_violaceus
     0.005480418 0.005480418
     Sericornis_citreogularis
     0.005480418 0.005386634
    
     0.005386634 0.005386634
     Alisterus_scapularis Calyptorhynchus_funereus
     0.001844732 0.001844732
     Leucosarcia_melanoleuca Petroica_rosea
     0.001844732 0.001844732
     Zoothera_lunulata Corvus_coronoides
     0.001844732 0.000000000
     Dacelo_novaeguineae Oriolus_sagittatus
     0.000000000 0.000000000
    
    > SPBoot(bird$inci, datatype="incidence_raw")
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    iNextPD
     --- call from context ---
    as.incfreq(x)
     --- call from argument ---
    if (class(x) == "data.frame" | class(x) == "matrix") {
     a <- sort(unique(c(unlist(x))))
     if (!identical(a, c(0, 1))) {
     warning("Invalid data type, the element of species by sites presence-absence matrix should be 0 or 1. Set nonzero elements as 1.")
     x <- (x > 0)
     }
     nT <- ncol(x)
     y <- rowSums(x)
     y <- c(nT, y)
     y
    } else if (class(x) == "numeric" | class(x) == "integer" | class(x) ==
     "double") {
     warnings("Ambiguous data type, the input object is a vector. Set total number of sampling units as 1.")
     c(1, x)
    } else {
     stop("Invalid data type, it should be a data.frame or matrix.")
    }
     --- R stacktrace ---
    where 1: as.incfreq(x)
    where 2: SPBoot_(x, datatype)
    where 3: FUN(X[[i]], ...)
    where 4: lapply(x, function(x) SPBoot_(x, datatype))
    where 5: SPBoot(bird$inci, datatype = "incidence_raw")
    
     --- value of length: 2 type: logical ---
    [1] TRUE FALSE
     --- function from context ---
    function (x)
    {
     if (class(x) == "data.frame" | class(x) == "matrix") {
     a <- sort(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: 0x4653a68>
    <environment: namespace:iNextPD>
     --- function search by body ---
    Function as.incfreq in namespace iNextPD has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(x) == "data.frame" | class(x) == "matrix") { :
     the condition has length > 1
    Calls: SPBoot -> lapply -> FUN -> SPBoot_ -> as.incfreq
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.3.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'Introduction.Rmd' using rmarkdown
    
    Attaching package: 'iNextPD'
    
    The following object is masked from 'package:iNEXT':
    
     ggiNEXT
    
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    iNextPD
     --- call from context ---
    as.incfreq(x)
     --- call from argument ---
    if (class(x) == "data.frame" | class(x) == "matrix") {
     a <- sort(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: as.incfreq(x)
    where 2: myFun0(x, U, L, datatype)
    where 3: FUN(X[[i]], ...)
    where 4: lapply(x, myFun, labels, phy, datatype)
    where 5: do.call("rbind", lapply(x, myFun, labels, phy, datatype))
    where 6: estPD(x, labels, phy, q = 0, datatype, se = TRUE, conf = conf)
    where 7: as.matrix(estPD(x, labels, phy, q = 0, datatype, se = TRUE, conf = conf))
    where 8: t(as.matrix(estPD(x, labels, phy, q = 0, datatype, se = TRUE,
     conf = conf)))
    where 9: iNextPD(bird$inci, bird.lab, bird.phy, q = 0, datatype = "incidence_raw",
     endpoint = 25, se = TRUE)
    where 10: eval(expr, envir, enclos)
    where 11: eval(expr, envir, enclos)
    where 12: withVisible(eval(expr, envir, enclos))
    where 13: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 14: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 15: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 16: evaluate_call(expr, parsed$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 17: evaluate::evaluate(...)
    where 18: 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$render,
     options))
    where 19: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
     keep_warning = !isFALSE(options$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 20: block_exec(params)
    where 21: call_block(x)
    where 22: process_group.block(group)
    where 23: process_group(group)
    where 24: 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$get("infile"),
     ") ")
     })
    where 25: process_file(text, output)
    where 26: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    where 27: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     ...)
    where 28: vweave_rmarkdown(...)
    where 29: engine$weave(file, quiet = quiet, encoding = enc)
    where 30: doTryCatch(return(expr), name, parentenv, handler)
    where 31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 32: tryCatchList(expr, classes, parentenv, handlers)
    where 33: 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 34: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/iNextPD.Rcheck/vign_test/iNextPD",
     ser_elibs = "/tmp/RtmpVh8QO1/file2db63dd08413.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(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: 0x83398f8>
    <environment: namespace:iNextPD>
     --- function search by body ---
    Function as.incfreq in namespace iNextPD has this body.
     ----------- END OF FAILURE REPORT --------------
    Quitting from lines 332-340 (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: In if (class(x) == "data.frame" | class(x) == "matrix") { :
     the condition has length > 1 and only the first element will be used
    2: In if (class(x) == "data.frame" | class(x) == "matrix") { :
     the condition has length > 1 and only the first element will be used
    3: In if (class(x) == "data.frame" | class(x) == "matrix") { :
     the condition has length > 1 and only the first element will be used
    4: In if (class(x) == "data.frame" | class(x) == "matrix") { :
     the condition has length > 1 and only the first element will be used
    5: In if (class(x) == "data.frame" | class(x) == "matrix") { :
     the condition has length > 1 and only the first element will be used
    6: In if (class(x) == "data.frame" | class(x) == "matrix") { :
     the condition has length > 1 and only the first element will be used
    7: In if (class(x) == "data.frame" | class(x) == "matrix") { :
     the condition has length > 1 and only the first element will be used
    8: In if (class(x) == "data.frame" | class(x) == "matrix") { :
     the condition has length > 1 and only the first element will be used
    9: In if (class(x) == "data.frame" | class(x) == "matrix") { :
     the condition has length > 1 and only the first element will be used
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang