CRAN Package Check Results for Package treeplyr

Last updated on 2020-05-29 10:47:37 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.7 20.67 86.59 107.26 ERROR
r-devel-linux-x86_64-debian-gcc 0.1.7 16.91 65.76 82.67 ERROR
r-devel-linux-x86_64-fedora-clang 0.1.7 140.73 ERROR
r-devel-linux-x86_64-fedora-gcc 0.1.7 126.82 ERROR
r-devel-windows-ix86+x86_64 0.1.7 68.00 155.00 223.00 ERROR
r-patched-linux-x86_64 0.1.7 18.27 86.93 105.20 OK
r-patched-solaris-x86 0.1.7 183.10 OK
r-release-linux-x86_64 0.1.7 19.40 86.36 105.76 OK
r-release-osx-x86_64 0.1.7 OK
r-release-windows-ix86+x86_64 0.1.7 47.00 205.00 252.00 OK
r-oldrel-osx-x86_64 0.1.7 OK
r-oldrel-windows-ix86+x86_64 0.1.7 41.00 136.00 177.00 OK

Check Details

Version: 0.1.7
Check: examples
Result: ERROR
    Running examples in 'treeplyr-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: group_by_.treedata
    > ### Title: Function for grouping an object of class 'treedata'
    > ### Aliases: group_by_.treedata group_by.treedata ungroup.grouped_treedata
    >
    > ### ** Examples
    >
    > data(anolis)
    > td <- make.treedata(anolis$phy, anolis$dat)
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    > tdGrouped <- group_by(td, ecomorph)
    > summarize(tdGrouped, ntips = length(phy$tip.label),
    + totalBL = sum(phy$edge.length), meanSVL = mean(SVL), sdSVL = sd(SVL))
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Error in make.treedata(x, dat) : tree must be of class 'phylo'
    Calls: summarize ... summarise.grouped_treedata -> lapply -> FUN -> make.treedata
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.1.7
Check: examples
Result: ERROR
    Running examples in ‘treeplyr-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: group_by_.treedata
    > ### Title: Function for grouping an object of class 'treedata'
    > ### Aliases: group_by_.treedata group_by.treedata ungroup.grouped_treedata
    >
    > ### ** Examples
    >
    > data(anolis)
    > td <- make.treedata(anolis$phy, anolis$dat)
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    > tdGrouped <- group_by(td, ecomorph)
    > summarize(tdGrouped, ntips = length(phy$tip.label),
    + totalBL = sum(phy$edge.length), meanSVL = mean(SVL), sdSVL = sd(SVL))
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Error in make.treedata(x, dat) : tree must be of class 'phylo'
    Calls: summarize ... summarise.grouped_treedata -> lapply -> FUN -> make.treedata
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.1.7
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'treeplyr-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: group_by_.treedata
    > ### Title: Function for grouping an object of class 'treedata'
    > ### Aliases: group_by_.treedata group_by.treedata ungroup.grouped_treedata
    >
    > ### ** Examples
    >
    > data(anolis)
    > td <- make.treedata(anolis$phy, anolis$dat)
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    > tdGrouped <- group_by(td, ecomorph)
    > summarize(tdGrouped, ntips = length(phy$tip.label),
    + totalBL = sum(phy$edge.length), meanSVL = mean(SVL), sdSVL = sd(SVL))
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Error in make.treedata(x, dat) : tree must be of class 'phylo'
    Calls: summarize ... summarise.grouped_treedata -> lapply -> FUN -> make.treedata
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.1.7
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'treeplyr-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: group_by_.treedata
    > ### Title: Function for grouping an object of class 'treedata'
    > ### Aliases: group_by_.treedata group_by.treedata ungroup.grouped_treedata
    >
    > ### ** Examples
    >
    > data(anolis)
    > td <- make.treedata(anolis$phy, anolis$dat)
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    Warning in type.convert.default(apply(data[, x, drop = FALSE], 1, as.character)) :
     'as.is' should be specified by the caller; using TRUE
    > tdGrouped <- group_by(td, ecomorph)
    > summarize(tdGrouped, ntips = length(phy$tip.label),
    + totalBL = sum(phy$edge.length), meanSVL = mean(SVL), sdSVL = sd(SVL))
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Warning in group_index %in% as.numeric(x) : NAs introduced by coercion
    Warning in drop.tip(.data$phy, which(!(group_index %in% as.numeric(x)))) :
     drop all tips of the tree: returning NULL
    Error in make.treedata(x, dat) : tree must be of class 'phylo'
    Calls: summarize ... summarise.grouped_treedata -> lapply -> FUN -> make.treedata
    Execution halted
Flavor: r-devel-windows-ix86+x86_64