CRAN Package Check Results for Package lefko3

Last updated on 2020-09-08 06:54:40 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	2.3.0	93.48	130.83	224.31	OK
r-devel-linux-x86_64-debian-gcc	2.3.0	90.59	100.76	191.35	OK
r-devel-linux-x86_64-fedora-clang	2.3.0			322.40	NOTE
r-devel-linux-x86_64-fedora-gcc	2.3.0			317.16	OK
r-devel-windows-ix86+x86_64	2.3.0	220.00	205.00	425.00	OK
r-patched-linux-x86_64	2.3.0	101.04	131.55	232.59	OK
r-patched-solaris-x86	2.3.0			294.10	OK
r-release-linux-x86_64	2.3.0	103.59	131.51	235.10	OK
r-release-macos-x86_64	2.3.0				NOTE
r-release-windows-ix86+x86_64	2.3.0	215.00	206.00	421.00	OK
r-oldrel-macos-x86_64	2.3.0				ERROR
r-oldrel-windows-ix86+x86_64	2.3.0	142.00	180.00	322.00	ERROR

Additional issues

clang-ASAN gcc-ASAN valgrind

Check Details

Version: 2.3.0
Check: installed package size
Result: NOTE
     installed size is 8.1Mb
     sub-directories of 1Mb or more:
     doc 1.7Mb
     libs 5.8Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 2.3.0
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", "D", "XSm", "Sm", "SL", "SL"),
    + stage2 = c("SD", "SD", "P1", "P2", "P3", "P3", "P3", "P3", "SL"),
    + eststage3 = c(NA, NA, NA, NA, "D", "XSm", "Sm", NA, NA),
    + eststage2 = c(NA, NA, NA, NA, "D", "D", "D", NA, NA),
    + givenrate = c(0.1, 0.2, 0.2, 0.2, NA, NA, NA, 0.25, 0.4),
    + 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", "stage1"),
    + 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: 2.3.0
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", "D", "XSm", "Sm", "SL", "SL"),
    + stage2 = c("SD", "SD", "P1", "P2", "P3", "P3", "P3", "P3", "SL"),
    + eststage3 = c(NA, NA, NA, NA, "D", "XSm", "Sm", NA, NA),
    + eststage2 = c(NA, NA, NA, NA, "D", "D", "D", NA, NA),
    + givenrate = c(0.1, 0.2, 0.2, 0.2, NA, NA, NA, 0.25, 0.4),
    + 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", "stage1"),
    + 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: 2.3.0
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", "D", "XSm", "Sm", "SL", "SL"),
    + stage2 = c("SD", "SD", "P1", "P2", "P3", "P3", "P3", "P3", "SL"),
    + eststage3 = c(NA, NA, NA, NA, "D", "XSm", "Sm", NA, NA),
    + eststage2 = c(NA, NA, NA, NA, "D", "D", "D", NA, NA),
    + givenrate = c(0.1, 0.2, 0.2, 0.2, NA, NA, NA, 0.25, 0.4),
    + 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", "stage1"),
    + 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