CRAN Package Check Results for Package unmarked

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

Check Details

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