CRAN Package Check Results for Package lefko3

Last updated on 2020-10-11 01:47:24 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	2.4.2	106.73	136.31	243.04	OK
r-devel-linux-x86_64-debian-gcc	2.4.2	103.47	104.81	208.28	OK
r-devel-linux-x86_64-fedora-clang	2.4.2			331.51	NOTE
r-devel-linux-x86_64-fedora-gcc	2.4.2			346.84	OK
r-devel-windows-ix86+x86_64	2.4.2	235.00	171.00	406.00	NOTE
r-patched-linux-x86_64	2.4.2	110.58	128.81	239.39	OK
r-patched-solaris-x86	2.4.2			315.60	OK
r-release-linux-x86_64	2.4.2	114.10	127.97	242.07	OK
r-release-macos-x86_64	2.4.2				NOTE
r-release-windows-ix86+x86_64	2.4.2	173.00	212.00	385.00	NOTE
r-oldrel-macos-x86_64	2.4.2				ERROR
r-oldrel-windows-ix86+x86_64	2.4.2	206.00	143.00	349.00	ERROR

Check Details

Version: 2.4.2
Check: installed package size
Result: NOTE
     installed size is 9.2Mb
     sub-directories of 1Mb or more:
     doc 1.7Mb
     libs 6.9Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64

Version: 2.4.2
Check: examples
Result: ERROR
    Running examples in ‘lefko3-Ex.R’ failed
    The error most likely occurred in:

    > ### Name: cypdata
    > ### Title: Demographic Dataset of _Cypripedium candidum_ Population, in
    > ### Horizontal Format
    > ### Aliases: cypdata
    > ### Keywords: datasets
    >
    > ### ** Examples
    >
    > data(cypdata)
    >
    > sizevector <- c(0, 0, 0, 0, 0, 0, 1, 2.5, 4.5, 8, 17.5)
    > stagevector <- c("SD", "P1", "P2", "P3", "SL", "D", "XSm",
    + "Sm", "Md", "Lg", "XLg")
    > repvector <- c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
    > obsvector <- c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
    > matvector <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
    > immvector <- c(0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0)
    > propvector <- c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
    > indataset <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
    > binvec <- c(0, 0, 0, 0, 0, 0.5, 0.5, 1, 1, 2.5, 7)
    >
    > cypframe_raw <- sf_create(sizes = sizevector, stagenames = stagevector,
    + repstatus = repvector, obsstatus = obsvector,
    + matstatus = matvector, propstatus = propvector,
    + immstatus = immvector, indataset = indataset,
    + binhalfwidth = binvec)
    >
    > cypraw_v1 <- verticalize3(data = cypdata, noyears = 6, firstyear = 2004,
    + patchidcol = "patch", individcol = "plantid",
    + blocksize = 4, size1col = "Inf2.04", size2col = "Inf.04",
    + size3col = "Veg.04", repstr1col = "Inf.04",
    + repstr2col = "Inf2.04", fec1col = "Pod.04",
    + stageassign = cypframe_raw, stagesize = "sizeadded",
    + NAas0 = TRUE, NRasRep = TRUE)
    >
    > rep_cyp_raw <- matrix(0, 11, 11)
    > rep_cyp_raw[1:2,7:11] <- 0.5
    >
    > cypover2r <- overwrite(stage3 = c("SD", "P1", "P2", "P3", "SL", "SL", "D",
    + "XSm", "Sm"), stage2 = c("SD", "SD", "P1", "P2", "P3",
    + "SL", "SL", "SL", "SL"), eststage3 = c(NA, NA, NA, NA,
    + NA, NA, "D", "XSm", "Sm"), eststage2 = c(NA, NA, NA, NA,
    + NA, NA, "XSm", "XSm", "XSm"), givenrate = c(0.1, 0.2,
    + 0.2, 0.2, 0.25, 0.4, NA, NA, NA), type = c("S", "S", "S",
    + "S", "S", "S", "S", "S", "S"))
    >
    > cypmatrix2r <- rlefko2(data = cypraw_v1, stageframe = cypframe_raw, year = "all",
    + patch = "all", stages = c("stage3", "stage2"),
    + size = c("size3added", "size2added"),
    + repmatrix = rep_cyp_raw, overwrite = cypover2r,
    + yearcol = "year2", patchcol = "patchid",
    + indivcol = "individ")
    Warning in `[<-.factor`(`*tmp*`, ri, value = "Dead") :
     invalid factor level, NA generated
    Warning in `[<-.factor`(`*tmp*`, which(data$usedstage3 == "NotAlive"), value = "Dead") :
     invalid factor level, NA generated
    Error in rlefko2(data = cypraw_v1, stageframe = cypframe_raw, year = "all", :
     Some stages in dataset do not match those detailed in the input stageframe.FALSE
    Execution halted
Flavor: r-oldrel-macos-x86_64

Version: 2.4.2
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'lefko3-Ex.R' failed
    The error most likely occurred in:

    > ### Name: cypdata
    > ### Title: Demographic Dataset of _Cypripedium candidum_ Population, in
    > ### Horizontal Format
    > ### Aliases: cypdata
    > ### Keywords: datasets
    >
    > ### ** Examples
    >
    > data(cypdata)
    >
    > sizevector <- c(0, 0, 0, 0, 0, 0, 1, 2.5, 4.5, 8, 17.5)
    > stagevector <- c("SD", "P1", "P2", "P3", "SL", "D", "XSm",
    + "Sm", "Md", "Lg", "XLg")
    > repvector <- c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
    > obsvector <- c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
    > matvector <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
    > immvector <- c(0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0)
    > propvector <- c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
    > indataset <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
    > binvec <- c(0, 0, 0, 0, 0, 0.5, 0.5, 1, 1, 2.5, 7)
    >
    > cypframe_raw <- sf_create(sizes = sizevector, stagenames = stagevector,
    + repstatus = repvector, obsstatus = obsvector,
    + matstatus = matvector, propstatus = propvector,
    + immstatus = immvector, indataset = indataset,
    + binhalfwidth = binvec)
    >
    > cypraw_v1 <- verticalize3(data = cypdata, noyears = 6, firstyear = 2004,
    + patchidcol = "patch", individcol = "plantid",
    + blocksize = 4, size1col = "Inf2.04", size2col = "Inf.04",
    + size3col = "Veg.04", repstr1col = "Inf.04",
    + repstr2col = "Inf2.04", fec1col = "Pod.04",
    + stageassign = cypframe_raw, stagesize = "sizeadded",
    + NAas0 = TRUE, NRasRep = TRUE)
    >
    > rep_cyp_raw <- matrix(0, 11, 11)
    > rep_cyp_raw[1:2,7:11] <- 0.5
    >
    > cypover2r <- overwrite(stage3 = c("SD", "P1", "P2", "P3", "SL", "SL", "D",
    + "XSm", "Sm"), stage2 = c("SD", "SD", "P1", "P2", "P3",
    + "SL", "SL", "SL", "SL"), eststage3 = c(NA, NA, NA, NA,
    + NA, NA, "D", "XSm", "Sm"), eststage2 = c(NA, NA, NA, NA,
    + NA, NA, "XSm", "XSm", "XSm"), givenrate = c(0.1, 0.2,
    + 0.2, 0.2, 0.25, 0.4, NA, NA, NA), type = c("S", "S", "S",
    + "S", "S", "S", "S", "S", "S"))
    >
    > cypmatrix2r <- rlefko2(data = cypraw_v1, stageframe = cypframe_raw, year = "all",
    + patch = "all", stages = c("stage3", "stage2"),
    + size = c("size3added", "size2added"),
    + repmatrix = rep_cyp_raw, overwrite = cypover2r,
    + yearcol = "year2", patchcol = "patchid",
    + indivcol = "individ")
    Warning in `[<-.factor`(`*tmp*`, ri, value = "Dead") :
     invalid factor level, NA generated
    Warning in `[<-.factor`(`*tmp*`, which(data$usedstage3 == "NotAlive"), value = "Dead") :
     invalid factor level, NA generated
    Error in rlefko2(data = cypraw_v1, stageframe = cypframe_raw, year = "all", :
     Some stages in dataset do not match those detailed in the input stageframe.FALSE
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 2.4.2
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'lefko3-Ex.R' failed
    The error most likely occurred in:

    > ### Name: cypdata
    > ### Title: Demographic Dataset of _Cypripedium candidum_ Population, in
    > ### Horizontal Format
    > ### Aliases: cypdata
    > ### Keywords: datasets
    >
    > ### ** Examples
    >
    > data(cypdata)
    >
    > sizevector <- c(0, 0, 0, 0, 0, 0, 1, 2.5, 4.5, 8, 17.5)
    > stagevector <- c("SD", "P1", "P2", "P3", "SL", "D", "XSm",
    + "Sm", "Md", "Lg", "XLg")
    > repvector <- c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
    > obsvector <- c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
    > matvector <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
    > immvector <- c(0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0)
    > propvector <- c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
    > indataset <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
    > binvec <- c(0, 0, 0, 0, 0, 0.5, 0.5, 1, 1, 2.5, 7)
    >
    > cypframe_raw <- sf_create(sizes = sizevector, stagenames = stagevector,
    + repstatus = repvector, obsstatus = obsvector,
    + matstatus = matvector, propstatus = propvector,
    + immstatus = immvector, indataset = indataset,
    + binhalfwidth = binvec)
    >
    > cypraw_v1 <- verticalize3(data = cypdata, noyears = 6, firstyear = 2004,
    + patchidcol = "patch", individcol = "plantid",
    + blocksize = 4, size1col = "Inf2.04", size2col = "Inf.04",
    + size3col = "Veg.04", repstr1col = "Inf.04",
    + repstr2col = "Inf2.04", fec1col = "Pod.04",
    + stageassign = cypframe_raw, stagesize = "sizeadded",
    + NAas0 = TRUE, NRasRep = TRUE)
    >
    > rep_cyp_raw <- matrix(0, 11, 11)
    > rep_cyp_raw[1:2,7:11] <- 0.5
    >
    > cypover2r <- overwrite(stage3 = c("SD", "P1", "P2", "P3", "SL", "SL", "D",
    + "XSm", "Sm"), stage2 = c("SD", "SD", "P1", "P2", "P3",
    + "SL", "SL", "SL", "SL"), eststage3 = c(NA, NA, NA, NA,
    + NA, NA, "D", "XSm", "Sm"), eststage2 = c(NA, NA, NA, NA,
    + NA, NA, "XSm", "XSm", "XSm"), givenrate = c(0.1, 0.2,
    + 0.2, 0.2, 0.25, 0.4, NA, NA, NA), type = c("S", "S", "S",
    + "S", "S", "S", "S", "S", "S"))
    >
    > cypmatrix2r <- rlefko2(data = cypraw_v1, stageframe = cypframe_raw, year = "all",
    + patch = "all", stages = c("stage3", "stage2"),
    + size = c("size3added", "size2added"),
    + repmatrix = rep_cyp_raw, overwrite = cypover2r,
    + yearcol = "year2", patchcol = "patchid",
    + indivcol = "individ")
    Warning in `[<-.factor`(`*tmp*`, ri, value = "Dead") :
     invalid factor level, NA generated
    Warning in `[<-.factor`(`*tmp*`, which(data$usedstage3 == "NotAlive"), value = "Dead") :
     invalid factor level, NA generated
    Error in rlefko2(data = cypraw_v1, stageframe = cypframe_raw, year = "all", :
     Some stages in dataset do not match those detailed in the input stageframe.FALSE
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64