CRAN Package Check Results for Package fossil

Last updated on 2020-02-25 15:47:54 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3.7 5.62 39.85 45.47 ERROR
r-devel-linux-x86_64-debian-gcc 0.3.7 4.10 31.96 36.06 ERROR
r-devel-linux-x86_64-fedora-clang 0.3.7 57.27 ERROR
r-devel-linux-x86_64-fedora-gcc 0.3.7 53.60 ERROR
r-devel-windows-ix86+x86_64 0.3.7 9.00 72.00 81.00 NOTE
r-devel-windows-ix86+x86_64-gcc8 0.3.7 10.00 71.00 81.00 NOTE
r-patched-linux-x86_64 0.3.7 5.10 50.31 55.41 NOTE
r-patched-solaris-x86 0.3.7 87.50 NOTE
r-release-linux-x86_64 0.3.7 5.04 50.57 55.61 NOTE
r-release-windows-ix86+x86_64 0.3.7 9.00 62.00 71.00 NOTE
r-release-osx-x86_64 0.3.7 NOTE
r-oldrel-windows-ix86+x86_64 0.3.7 9.00 65.00 74.00 NOTE
r-oldrel-osx-x86_64 0.3.7 NOTE

Check Details

Version: 0.3.7
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to 'shapefiles' which was already attached by Depends.
     Please remove these calls from your code.
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: 0.3.7
Check: R code for possible problems
Result: NOTE
    dino.dist: no visible global function definition for 'as.dist'
    earth.dist: no visible global function definition for 'as.dist'
    ecol.dist: no visible global function definition for 'as.dist'
    loc.map: no visible global function definition for 'points'
    msn.map: no visible global function definition for 'points'
    msn.map: no visible global function definition for 'lines'
    mstlines: no visible global function definition for 'lines'
    nmds.mst: no visible global function definition for 'lines'
    rclust.null: no visible global function definition for 'sd'
    sim.occ: no visible global function definition for 'rlnorm'
    spp.est: no visible global function definition for 'sd'
    Undefined global functions or variables:
     as.dist lines points rlnorm sd
    Consider adding
     importFrom("graphics", "lines", "points")
     importFrom("stats", "as.dist", "rlnorm", "sd")
    to your NAMESPACE file.
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: 0.3.7
Check: Rd line widths
Result: NOTE
    Rd file 'create.matrix.Rd':
     \usage lines wider than 90 characters:
     create.matrix(x,tax.name="genus",locality="locality",time.col=NULL,time=NULL,abund=FALSE,abund.col="abundance")
    
    Rd file 'new.lat.long.Rd':
     \examples lines wider than 100 characters:
     #Travel from 0,0 to a new location at a bearing of 45 degrees from North (clockwise) and 1000 km away
    
    These lines will be truncated in the PDF manual.
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-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.3.7
Check: examples
Result: ERROR
    Running examples in 'fossil-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: earth.poly
    > ### Title: Calculating a Minimum Convex Polygon
    > ### Aliases: earth.poly
    > ### Keywords: graphs
    >
    > ### ** Examples
    >
    > #1/8th the surface area of the earth
    > a <- matrix(c(0, 0, 0, 90, 90, 0, 25, 25), 4, 2, byrow = TRUE)
    > earth.poly(a)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    fossil
     --- call from context ---
    earth.poly(a)
     --- call from argument ---
    if (class(lats) == "SpatialPoints") lats <- coordinates(lats)
     --- R stacktrace ---
    where 1: earth.poly(a)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (lats)
    {
     if (class(lats) == "SpatialPoints")
     lats <- coordinates(lats)
     lats <- unique(lats)
     rownames.lats <- rownames(lats)
     nr <- nrow(lats)
     bm <- matrix(, nr, nr)
     for (i in 1:nr) {
     for (j in 1:nr) {
     if (i == j)
     bm[i, j] <- -1
     else bm[i, j] <- earth.bear(long1 = lats[i, 1], lat1 = lats[i,
     2], long2 = lats[j, 1], lat2 = lats[j, 2])
     }
     }
     qm <- matrix(, nr, 4)
     for (i in 1:nr) {
     qm[i, 1] <- length(bm[1, ][bm[i, ] >= 0]) - length(bm[i,
     ][bm[i, ] >= 90])
     qm[i, 2] <- length(bm[1, ][bm[i, ] >= 90]) - length(bm[i,
     ][bm[i, ] >= 180])
     qm[i, 3] <- length(bm[1, ][bm[i, ] >= 180]) - length(bm[i,
     ][bm[i, ] >= 270])
     qm[i, 4] <- length(bm[1, ][bm[i, ] >= 270])
     }
     id <- numeric(nr)
     for (i in 1:nr) {
     for (j in 1:4) {
     if (length(qm[i, ][qm[i, ] > 0]) <= 2)
     id[i] <- i
     else {
     if (length(qm[i, ][qm[i, ] > 0]) == 3) {
     if (length(qm[i, 2:3][qm[i, 2:3] > 0]) == 2) {
     if ((max(bm[i, ]) - min(bm[i, ][bm[i, ] >=
     0])) < 180)
     id[i] <- i
     }
     else {
     if ((360 - min(bm[i, ][bm[i, ] > 180]) +
     max(bm[i, ][bm[i, ] < 180])) < 180)
     id[i] <- i
     }
     }
     }
     }
     }
     mi <- id[id > 0]
     prpt <- mi[1]
     snpts <- mi[-1]
     pt <- bm[prpt, snpts]
     if ((max(pt) - min(pt)) > 180) {
     pt[pt < 180] <- pt[pt < 180] + 360
     }
     rpt <- rank(pt)
     ind <- numeric(length(pt))
     for (i in 1:length(pt)) ind[rpt[i]] <- snpts[i]
     ta <- numeric(1)
     for (i in 1:(length(pt) - 1)) {
     k <- i + 1
     ta <- ta + earth.tri(long1 = lats[prpt, 1], lat1 = lats[prpt,
     2], long2 = lats[ind[i], 1], lat2 = lats[ind[i],
     2], long3 = lats[ind[k], 1], lat3 = lats[ind[k],
     2])
     }
     verts <- c(prpt, ind)
     return(list(area = ta, vertices = verts))
    }
    <bytecode: 0x8f0bb8>
    <environment: namespace:fossil>
     --- function search by body ---
    Function earth.poly in namespace fossil has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(lats) == "SpatialPoints") lats <- coordinates(lats) :
     the condition has length > 1
    Calls: earth.poly
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.3.7
Check: examples
Result: ERROR
    Running examples in ‘fossil-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: earth.poly
    > ### Title: Calculating a Minimum Convex Polygon
    > ### Aliases: earth.poly
    > ### Keywords: graphs
    >
    > ### ** Examples
    >
    > #1/8th the surface area of the earth
    > a <- matrix(c(0, 0, 0, 90, 90, 0, 25, 25), 4, 2, byrow = TRUE)
    > earth.poly(a)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    fossil
     --- call from context ---
    earth.poly(a)
     --- call from argument ---
    if (class(lats) == "SpatialPoints") lats <- coordinates(lats)
     --- R stacktrace ---
    where 1: earth.poly(a)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (lats)
    {
     if (class(lats) == "SpatialPoints")
     lats <- coordinates(lats)
     lats <- unique(lats)
     rownames.lats <- rownames(lats)
     nr <- nrow(lats)
     bm <- matrix(, nr, nr)
     for (i in 1:nr) {
     for (j in 1:nr) {
     if (i == j)
     bm[i, j] <- -1
     else bm[i, j] <- earth.bear(long1 = lats[i, 1], lat1 = lats[i,
     2], long2 = lats[j, 1], lat2 = lats[j, 2])
     }
     }
     qm <- matrix(, nr, 4)
     for (i in 1:nr) {
     qm[i, 1] <- length(bm[1, ][bm[i, ] >= 0]) - length(bm[i,
     ][bm[i, ] >= 90])
     qm[i, 2] <- length(bm[1, ][bm[i, ] >= 90]) - length(bm[i,
     ][bm[i, ] >= 180])
     qm[i, 3] <- length(bm[1, ][bm[i, ] >= 180]) - length(bm[i,
     ][bm[i, ] >= 270])
     qm[i, 4] <- length(bm[1, ][bm[i, ] >= 270])
     }
     id <- numeric(nr)
     for (i in 1:nr) {
     for (j in 1:4) {
     if (length(qm[i, ][qm[i, ] > 0]) <= 2)
     id[i] <- i
     else {
     if (length(qm[i, ][qm[i, ] > 0]) == 3) {
     if (length(qm[i, 2:3][qm[i, 2:3] > 0]) == 2) {
     if ((max(bm[i, ]) - min(bm[i, ][bm[i, ] >=
     0])) < 180)
     id[i] <- i
     }
     else {
     if ((360 - min(bm[i, ][bm[i, ] > 180]) +
     max(bm[i, ][bm[i, ] < 180])) < 180)
     id[i] <- i
     }
     }
     }
     }
     }
     mi <- id[id > 0]
     prpt <- mi[1]
     snpts <- mi[-1]
     pt <- bm[prpt, snpts]
     if ((max(pt) - min(pt)) > 180) {
     pt[pt < 180] <- pt[pt < 180] + 360
     }
     rpt <- rank(pt)
     ind <- numeric(length(pt))
     for (i in 1:length(pt)) ind[rpt[i]] <- snpts[i]
     ta <- numeric(1)
     for (i in 1:(length(pt) - 1)) {
     k <- i + 1
     ta <- ta + earth.tri(long1 = lats[prpt, 1], lat1 = lats[prpt,
     2], long2 = lats[ind[i], 1], lat2 = lats[ind[i],
     2], long3 = lats[ind[k], 1], lat3 = lats[ind[k],
     2])
     }
     verts <- c(prpt, ind)
     return(list(area = ta, vertices = verts))
    }
    <bytecode: 0x55b615430f40>
    <environment: namespace:fossil>
     --- function search by body ---
    Function earth.poly in namespace fossil has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(lats) == "SpatialPoints") lats <- coordinates(lats) :
     the condition has length > 1
    Calls: earth.poly
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.3.7
Check: examples
Result: ERROR
    Running examples in ‘fossil-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: earth.poly
    > ### Title: Calculating a Minimum Convex Polygon
    > ### Aliases: earth.poly
    > ### Keywords: graphs
    >
    > ### ** Examples
    >
    > #1/8th the surface area of the earth
    > a <- matrix(c(0, 0, 0, 90, 90, 0, 25, 25), 4, 2, byrow = TRUE)
    > earth.poly(a)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    fossil
     --- call from context ---
    earth.poly(a)
     --- call from argument ---
    if (class(lats) == "SpatialPoints") lats <- coordinates(lats)
     --- R stacktrace ---
    where 1: earth.poly(a)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (lats)
    {
     if (class(lats) == "SpatialPoints")
     lats <- coordinates(lats)
     lats <- unique(lats)
     rownames.lats <- rownames(lats)
     nr <- nrow(lats)
     bm <- matrix(, nr, nr)
     for (i in 1:nr) {
     for (j in 1:nr) {
     if (i == j)
     bm[i, j] <- -1
     else bm[i, j] <- earth.bear(long1 = lats[i, 1], lat1 = lats[i,
     2], long2 = lats[j, 1], lat2 = lats[j, 2])
     }
     }
     qm <- matrix(, nr, 4)
     for (i in 1:nr) {
     qm[i, 1] <- length(bm[1, ][bm[i, ] >= 0]) - length(bm[i,
     ][bm[i, ] >= 90])
     qm[i, 2] <- length(bm[1, ][bm[i, ] >= 90]) - length(bm[i,
     ][bm[i, ] >= 180])
     qm[i, 3] <- length(bm[1, ][bm[i, ] >= 180]) - length(bm[i,
     ][bm[i, ] >= 270])
     qm[i, 4] <- length(bm[1, ][bm[i, ] >= 270])
     }
     id <- numeric(nr)
     for (i in 1:nr) {
     for (j in 1:4) {
     if (length(qm[i, ][qm[i, ] > 0]) <= 2)
     id[i] <- i
     else {
     if (length(qm[i, ][qm[i, ] > 0]) == 3) {
     if (length(qm[i, 2:3][qm[i, 2:3] > 0]) == 2) {
     if ((max(bm[i, ]) - min(bm[i, ][bm[i, ] >=
     0])) < 180)
     id[i] <- i
     }
     else {
     if ((360 - min(bm[i, ][bm[i, ] > 180]) +
     max(bm[i, ][bm[i, ] < 180])) < 180)
     id[i] <- i
     }
     }
     }
     }
     }
     mi <- id[id > 0]
     prpt <- mi[1]
     snpts <- mi[-1]
     pt <- bm[prpt, snpts]
     if ((max(pt) - min(pt)) > 180) {
     pt[pt < 180] <- pt[pt < 180] + 360
     }
     rpt <- rank(pt)
     ind <- numeric(length(pt))
     for (i in 1:length(pt)) ind[rpt[i]] <- snpts[i]
     ta <- numeric(1)
     for (i in 1:(length(pt) - 1)) {
     k <- i + 1
     ta <- ta + earth.tri(long1 = lats[prpt, 1], lat1 = lats[prpt,
     2], long2 = lats[ind[i], 1], lat2 = lats[ind[i],
     2], long3 = lats[ind[k], 1], lat3 = lats[ind[k],
     2])
     }
     verts <- c(prpt, ind)
     return(list(area = ta, vertices = verts))
    }
    <bytecode: 0x40f3008>
    <environment: namespace:fossil>
     --- function search by body ---
    Function earth.poly in namespace fossil has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(lats) == "SpatialPoints") lats <- coordinates(lats) :
     the condition has length > 1
    Calls: earth.poly
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.3.7
Check: examples
Result: ERROR
    Running examples in ‘fossil-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: earth.poly
    > ### Title: Calculating a Minimum Convex Polygon
    > ### Aliases: earth.poly
    > ### Keywords: graphs
    >
    > ### ** Examples
    >
    > #1/8th the surface area of the earth
    > a <- matrix(c(0, 0, 0, 90, 90, 0, 25, 25), 4, 2, byrow = TRUE)
    > earth.poly(a)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    fossil
     --- call from context ---
    earth.poly(a)
     --- call from argument ---
    if (class(lats) == "SpatialPoints") lats <- coordinates(lats)
     --- R stacktrace ---
    where 1: earth.poly(a)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (lats)
    {
     if (class(lats) == "SpatialPoints")
     lats <- coordinates(lats)
     lats <- unique(lats)
     rownames.lats <- rownames(lats)
     nr <- nrow(lats)
     bm <- matrix(, nr, nr)
     for (i in 1:nr) {
     for (j in 1:nr) {
     if (i == j)
     bm[i, j] <- -1
     else bm[i, j] <- earth.bear(long1 = lats[i, 1], lat1 = lats[i,
     2], long2 = lats[j, 1], lat2 = lats[j, 2])
     }
     }
     qm <- matrix(, nr, 4)
     for (i in 1:nr) {
     qm[i, 1] <- length(bm[1, ][bm[i, ] >= 0]) - length(bm[i,
     ][bm[i, ] >= 90])
     qm[i, 2] <- length(bm[1, ][bm[i, ] >= 90]) - length(bm[i,
     ][bm[i, ] >= 180])
     qm[i, 3] <- length(bm[1, ][bm[i, ] >= 180]) - length(bm[i,
     ][bm[i, ] >= 270])
     qm[i, 4] <- length(bm[1, ][bm[i, ] >= 270])
     }
     id <- numeric(nr)
     for (i in 1:nr) {
     for (j in 1:4) {
     if (length(qm[i, ][qm[i, ] > 0]) <= 2)
     id[i] <- i
     else {
     if (length(qm[i, ][qm[i, ] > 0]) == 3) {
     if (length(qm[i, 2:3][qm[i, 2:3] > 0]) == 2) {
     if ((max(bm[i, ]) - min(bm[i, ][bm[i, ] >=
     0])) < 180)
     id[i] <- i
     }
     else {
     if ((360 - min(bm[i, ][bm[i, ] > 180]) +
     max(bm[i, ][bm[i, ] < 180])) < 180)
     id[i] <- i
     }
     }
     }
     }
     }
     mi <- id[id > 0]
     prpt <- mi[1]
     snpts <- mi[-1]
     pt <- bm[prpt, snpts]
     if ((max(pt) - min(pt)) > 180) {
     pt[pt < 180] <- pt[pt < 180] + 360
     }
     rpt <- rank(pt)
     ind <- numeric(length(pt))
     for (i in 1:length(pt)) ind[rpt[i]] <- snpts[i]
     ta <- numeric(1)
     for (i in 1:(length(pt) - 1)) {
     k <- i + 1
     ta <- ta + earth.tri(long1 = lats[prpt, 1], lat1 = lats[prpt,
     2], long2 = lats[ind[i], 1], lat2 = lats[ind[i],
     2], long3 = lats[ind[k], 1], lat3 = lats[ind[k],
     2])
     }
     verts <- c(prpt, ind)
     return(list(area = ta, vertices = verts))
    }
    <bytecode: 0x399c5b0>
    <environment: namespace:fossil>
     --- function search by body ---
    Function earth.poly in namespace fossil has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(lats) == "SpatialPoints") lats <- coordinates(lats) :
     the condition has length > 1
    Calls: earth.poly
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc