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 |
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