Last updated on 2019-12-09 05:47:33 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.13-0 | 252.43 | 248.13 | 500.56 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.13-0 | 174.69 | 208.50 | 383.19 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.13-0 | 712.20 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.13-0 | 664.76 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 0.13-0 | 405.00 | 491.00 | 896.00 | NOTE | |
| r-devel-windows-ix86+x86_64-gcc8 | 0.13-0 | 513.00 | 396.00 | 909.00 | NOTE | |
| r-patched-linux-x86_64 | 0.13-0 | 190.84 | 248.30 | 439.14 | NOTE | |
| r-patched-solaris-x86 | 0.13-0 | 709.20 | NOTE | |||
| r-release-linux-x86_64 | 0.13-0 | 195.28 | 246.35 | 441.63 | NOTE | |
| r-release-windows-ix86+x86_64 | 0.13-0 | 495.00 | 350.00 | 845.00 | NOTE | |
| r-release-osx-x86_64 | 0.13-0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 0.13-0 | 338.00 | 309.00 | 647.00 | NOTE | |
| r-oldrel-osx-x86_64 | 0.13-0 | NOTE |
Version: 0.13-0
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64
Version: 0.13-0
Check: examples
Result: ERROR
Running examples in 'unmarked-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: colext
> ### Title: Fit the dynamic occupancy model of MacKenzie et. al (2003)
> ### Aliases: colext
> ### Keywords: models
>
> ### ** Examples
>
>
> # Fake data
> R <- 4 # number of sites
> J <- 3 # number of secondary sampling occasions
> T <- 2 # number of primary periods
>
> y <- matrix(c(
+ 1,1,0, 0,0,0,
+ 0,0,0, 0,0,0,
+ 1,1,1, 1,1,0,
+ 1,0,1, 0,0,1), nrow=R, ncol=J*T, byrow=TRUE)
> y
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1 1 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 1 1 1 1 1 0
[4,] 1 0 1 0 0 1
>
> site.covs <- data.frame(x1=1:4, x2=factor(c('A','B','A','B')))
> site.covs
x1 x2
1 1 A
2 2 B
3 3 A
4 4 B
>
> yearly.site.covs <- list(
+ year = matrix(c(
+ 'year1', 'year2',
+ 'year1', 'year2',
+ 'year1', 'year2',
+ 'year1', 'year2'), nrow=R, ncol=T, byrow=TRUE)
+ )
> yearly.site.covs
$year
[,1] [,2]
[1,] "year1" "year2"
[2,] "year1" "year2"
[3,] "year1" "year2"
[4,] "year1" "year2"
>
> obs.covs <- list(
+ x4 = matrix(c(
+ -1,0,1, -1,1,1,
+ -2,0,0, 0,0,2,
+ -3,1,0, 1,1,2,
+ 0,0,0, 0,1,-1), nrow=R, ncol=J*T, byrow=TRUE),
+ x5 = matrix(c(
+ 'a','b','c', 'a','b','c',
+ 'd','b','a', 'd','b','a',
+ 'a','a','c', 'd','b','a',
+ 'a','b','a', 'd','b','a'), nrow=R, ncol=J*T, byrow=TRUE))
> obs.covs
$x4
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -1 0 1 -1 1 1
[2,] -2 0 0 0 0 2
[3,] -3 1 0 1 1 2
[4,] 0 0 0 0 1 -1
$x5
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] "a" "b" "c" "a" "b" "c"
[2,] "d" "b" "a" "d" "b" "a"
[3,] "a" "a" "c" "d" "b" "a"
[4,] "a" "b" "a" "d" "b" "a"
>
> umf <- unmarkedMultFrame(y=y, siteCovs=site.covs,
+ yearlySiteCovs=yearly.site.covs, obsCovs=obs.covs,
+ numPrimary=2) # organize data
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
unmarked
--- call from context ---
unmarkedMultFrame(y = y, siteCovs = site.covs, yearlySiteCovs = yearly.site.covs,
obsCovs = obs.covs, numPrimary = 2)
--- call from argument ---
if (!(class(yearlySiteCovs[[i]]) %in% c("matrix", "data.frame"))) stop("At least one element of yearlySiteCovs is not a matrix or data frame.")
--- R stacktrace ---
where 1: unmarkedMultFrame(y = y, siteCovs = site.covs, yearlySiteCovs = yearly.site.covs,
obsCovs = obs.covs, numPrimary = 2)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (y, siteCovs = NULL, obsCovs = NULL, numPrimary, yearlySiteCovs = NULL)
{
J <- ncol(y)
umf <- unmarkedFrame(y, siteCovs, obsCovs, obsToY = diag(J))
umf <- as(umf, "unmarkedMultFrame")
umf@numPrimary <- numPrimary
if (class(yearlySiteCovs) == "list") {
yearlySiteVars <- names(yearlySiteCovs)
for (i in seq(length(yearlySiteVars))) {
if (!(class(yearlySiteCovs[[i]]) %in% c("matrix",
"data.frame")))
stop("At least one element of yearlySiteCovs is not a matrix or data frame.")
if (ncol(yearlySiteCovs[[i]]) != numPrimary | nrow(yearlySiteCovs[[i]]) !=
nrow(y))
stop("At least one matrix in yearlySiteCovs has incorrect number of dimensions.")
}
yearlySiteCovs <- data.frame(lapply(yearlySiteCovs, function(x) as.vector(t(x))))
}
umf@yearlySiteCovs <- yearlySiteCovs
umf
}
<bytecode: 0xfdb84d0>
<environment: namespace:unmarked>
--- function search by body ---
Function unmarkedMultFrame in namespace unmarked has this body.
----------- END OF FAILURE REPORT --------------
Error in if (!(class(yearlySiteCovs[[i]]) %in% c("matrix", "data.frame"))) stop("At least one element of yearlySiteCovs is not a matrix or data frame.") :
the condition has length > 1
Calls: unmarkedMultFrame
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.13-0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'cap-recap.Rnw' using Sweave
Loading required package: lattice
Loading required package: parallel
Loading required package: Rcpp
Loading required package: reshape2
--- finished re-building 'cap-recap.Rnw'
--- re-building 'colext.Rnw' using Sweave
Loading required package: lattice
Loading required package: parallel
Loading required package: Rcpp
Loading required package: reshape2
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
unmarked
--- call from context ---
unmarkedMultFrame(y = yy, yearlySiteCovs = list(year = year),
numPrimary = T)
--- call from argument ---
if (!(class(yearlySiteCovs[[i]]) %in% c("matrix", "data.frame"))) stop("At least one element of yearlySiteCovs is not a matrix or data frame.")
--- R stacktrace ---
where 1: unmarkedMultFrame(y = yy, yearlySiteCovs = list(year = year),
numPrimary = T)
where 2: eval(expr, .GlobalEnv)
where 3: eval(expr, .GlobalEnv)
where 4: withVisible(eval(expr, .GlobalEnv))
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 8: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 10: evalFunc(ce, options)
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 13: driver$runcode(drobj, chunk, chunkopts)
where 14: utils::Sweave(...)
where 15: engine$weave(file, quiet = quiet, encoding = enc)
where 16: doTryCatch(return(expr), name, parentenv, handler)
where 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 18: tryCatchList(expr, classes, parentenv, handlers)
where 19: tryCatch({
engine$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)
}
}, error = function(e) {
OK <<- FALSE
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 20: tools:::.buildOneVignette("colext.Rnw", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/unmarked.Rcheck/vign_test/unmarked",
TRUE, FALSE, "colext", "", "/tmp/RtmpmSm2tl/file4fe557efb195.rds")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (y, siteCovs = NULL, obsCovs = NULL, numPrimary, yearlySiteCovs = NULL)
{
J <- ncol(y)
umf <- unmarkedFrame(y, siteCovs, obsCovs, obsToY = diag(J))
umf <- as(umf, "unmarkedMultFrame")
umf@numPrimary <- numPrimary
if (class(yearlySiteCovs) == "list") {
yearlySiteVars <- names(yearlySiteCovs)
for (i in seq(length(yearlySiteVars))) {
if (!(class(yearlySiteCovs[[i]]) %in% c("matrix",
"data.frame")))
stop("At least one element of yearlySiteCovs is not a matrix or data frame.")
if (ncol(yearlySiteCovs[[i]]) != numPrimary | nrow(yearlySiteCovs[[i]]) !=
nrow(y))
stop("At least one matrix in yearlySiteCovs has incorrect number of dimensions.")
}
yearlySiteCovs <- data.frame(lapply(yearlySiteCovs, function(x) as.vector(t(x))))
}
umf@yearlySiteCovs <- yearlySiteCovs
umf
}
<bytecode: 0xf00a948>
<environment: namespace:unmarked>
--- function search by body ---
Function unmarkedMultFrame in namespace unmarked has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'colext.Rnw' failed with diagnostics:
chunk 7
Error in if (!(class(yearlySiteCovs[[i]]) %in% c("matrix", "data.frame"))) stop("At least one element of yearlySiteCovs is not a matrix or data frame.") :
the condition has length > 1
--- failed re-building 'colext.Rnw'
--- re-building 'distsamp.Rnw' using Sweave
Loading required package: lattice
Loading required package: parallel
Loading required package: Rcpp
Loading required package: reshape2
--- finished re-building 'distsamp.Rnw'
--- re-building 'spp-dist.Rnw' using Sweave
Loading required package: lattice
Loading required package: parallel
Loading required package: Rcpp
Loading required package: reshape2
Loading required package: sp
Attaching package: 'sp'
The following object is masked from 'package:unmarked':
coordinates
Attaching package: 'raster'
The following objects are masked from 'package:unmarked':
getData, projection
Warning: 22 sites have been discarded because of missing data.
--- finished re-building 'spp-dist.Rnw'
--- re-building 'unmarked.Rnw' using Sweave
Loading required package: lattice
Loading required package: parallel
Loading required package: Rcpp
Loading required package: reshape2
Warning in truncateToBinary(y) :
Some observations were > 1. These were truncated to 1.
Warning in truncateToBinary(y) :
Some observations were > 1. These were truncated to 1.
Warning in truncateToBinary(y) :
Some observations were > 1. These were truncated to 1.
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
--- finished re-building 'unmarked.Rnw'
SUMMARY: processing the following file failed:
'colext.Rnw'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.13-0
Check: installed package size
Result: NOTE
installed size is 12.6Mb
sub-directories of 1Mb or more:
R 1.3Mb
doc 1.6Mb
libs 8.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, 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