Last updated on 2020-03-13 16:46:59 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.13.0115 | 21.75 | 72.19 | 93.94 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.13.0115 | 15.15 | 56.01 | 71.16 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.13.0115 | 118.69 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.13.0115 | 112.07 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 0.13.0115 | 56.00 | 138.00 | 194.00 | NOTE | |
| r-devel-windows-ix86+x86_64-gcc8 | 0.13.0115 | 45.00 | 139.00 | 184.00 | NOTE | |
| r-patched-linux-x86_64 | 0.13.0115 | 16.85 | 70.75 | 87.60 | NOTE | |
| r-patched-solaris-x86 | 0.13.0115 | 188.80 | NOTE | |||
| r-release-linux-x86_64 | 0.13.0115 | 16.87 | 70.84 | 87.71 | NOTE | |
| r-release-windows-ix86+x86_64 | 0.13.0115 | 38.00 | 114.00 | 152.00 | NOTE | |
| r-release-osx-x86_64 | 0.13.0115 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 0.13.0115 | 32.00 | 108.00 | 140.00 | NOTE | |
| r-oldrel-osx-x86_64 | 0.13.0115 | NOTE |
Version: 0.13.0115
Check: dependencies in R code
Result: NOTE
Packages in Depends field not imported from:
'Rcpp' 'colorspace' 'picante'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
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: 0.13.0115
Check: R code for possible problems
Result: NOTE
add.transparency: no visible global function definition for 'col2rgb'
add.transparency: no visible global function definition for 'rgb'
as.phylocom: no visible global function definition for 'write.table'
as.picante: no visible global function definition for 'write.table'
as.spacodi: no visible global function definition for 'write.table'
cophen: no visible global function definition for 'Ntip'
get.descendants.of.node: no visible global function definition for
'Ntip'
phy.deresolve: no visible global function definition for
'branching.times'
phy.deresolve: no visible global function definition for 'Ntip'
phy.dotplot: no visible global function definition for 'par'
phy.dotplot: no visible global function definition for 'pdf'
phy.dotplot: no visible global function definition for 'layout'
phy.dotplot: no visible global function definition for 'tiplabels'
phy.dotplot: no visible global function definition for 'legend'
phy.dotplot: no visible global function definition for 'dev.off'
phy.dotplot: no visible global function definition for 'dev.new'
phy.nodetimes: no visible global function definition for 'Ntip'
phy.nodetimes: no visible global function definition for
'branching.times'
reorderspacodiobj: no visible global function definition for 'drop.tip'
resamp.1a: no visible global function definition for 'runif'
resamp.3t: no visible global function definition for 'runif'
resamp.phy: no visible global function definition for 'Ntip'
resamp.phy: no visible global function definition for 'branching.times'
spacodi.all.nodes: no visible global function definition for 'subtrees'
spacodi.all.nodes: no visible global function definition for
'branching.times'
spacodi.calc: no visible global function definition for 'dist'
spacodi.calc : <anonymous>: no visible global function definition for
'dist'
spacodi.exp.nodes: no visible global function definition for 'subtrees'
spacodi.permutplot: no visible global function definition for 'pdf'
spacodi.permutplot: no visible global function definition for 'points'
spacodi.permutplot: no visible global function definition for 'lines'
spacodi.permutplot: no visible global function definition for
'smooth.spline'
spacodi.permutplot: no visible global function definition for 'legend'
spacodi.permutplot: no visible global function definition for 'dev.off'
spacodi.treeplot: no visible global function definition for 'pdf'
spacodi.treeplot: no visible global function definition for
'diverge_hcl'
spacodi.treeplot: no visible global function definition for
'nodelabels'
spacodi.treeplot: no visible global function definition for 'legend'
spacodi.treeplot: no visible global function definition for 'title'
spacodi.treeplot: no visible global function definition for 'dev.off'
textxy: no visible global function definition for 'text'
write.spacodi.data: no visible global function definition for
'write.table'
Undefined global functions or variables:
Ntip branching.times col2rgb dev.new dev.off dist diverge_hcl
drop.tip layout legend lines nodelabels par pdf points rgb runif
smooth.spline subtrees text tiplabels title write.table
Consider adding
importFrom("grDevices", "col2rgb", "dev.new", "dev.off", "pdf", "rgb")
importFrom("graphics", "layout", "legend", "lines", "par", "points",
"text", "title")
importFrom("stats", "dist", "runif", "smooth.spline")
importFrom("utils", "write.table")
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-patched-solaris-x86
Version: 0.13.0115
Check: Rd line widths
Result: NOTE
Rd file 'phy.dotplot.Rd':
\usage lines wider than 90 characters:
phy.dotplot(sp.plot, phy, edge.width = 0.2, lab.adj = c(0, 0), tips.adj = c(0.5, 3), tips.cex = 1.0, pch = 21, print.labs = FALSE, outf ... [TRUNCATED]
Rd file 'spacodi.by.nodes.Rd':
\usage lines wider than 90 characters:
spacodi.by.nodes(sp.plot, phy, sp.parm = "Bst", obs.only = FALSE, return.all = TRUE, n.rep = 10, method = "1s", parm = NULL, dmat = NUL ... [TRUNCATED]
Rd file 'spacodi.calc.Rd':
\usage lines wider than 90 characters:
spacodi.calc(sp.plot, phy = NULL, sp.traits = NULL, all.together = TRUE, prune = TRUE, pairwise = FALSE, ...)
Rd file 'spacodi.permutplot.Rd':
\usage lines wider than 90 characters:
spacodi.permutplot(spacodi.permutations, cex=list(pch=1.5, rand=0.1, node=0.5, legend=0.75), transp=0.8, col = list("black", "lightgr ... [TRUNCATED]
bg = list("white", "lightgray", "black"), all.points = TRUE, add.id = TRUE, sig.plot = TRUE, cut.off = 0.05, envelope = FALSE, outfil ... [TRUNCATED]
Rd file 'spacodi.treeplot.Rd':
\usage lines wider than 90 characters:
spacodi.treeplot(spacodi.permutations, phy, cex=list(pch = 1.5, tip = 0.5, legend = 0.75), transp=0.8, sig.plot = TRUE, cut.off = 0.05, ... [TRUNCATED]
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: 0.13.0115
Check: examples
Result: ERROR
Running examples in 'spacodiR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: match.spacodi.data
> ### Title: pruning a tree to match datasets used in SPACoDi
> ### Aliases: match.spacodi.data
>
> ### ** Examples
>
> # load a species-by-plots matrix, along with a tree
> data(sp.example)
> attributes(sp.example)
$names
[1] "spl" "phy" "trt" "dis"
> attach(sp.example)
> spl
plot1 plot2 plot3 plot4 plot5 plot6 plot7 plot8 plot9 plot10
sp1 7 0 0 0 1 0 0 0 0 0
sp2 1 0 0 0 0 3 1 1 0 83
sp3 3 8 1 0 1 0 0 0 0 0
sp4 2 0 0 0 0 0 0 0 0 7
sp5 1 2 0 0 0 0 0 0 0 1
sp6 1 0 0 0 0 0 0 0 0 0
sp7 1 0 0 0 0 0 0 0 0 14
sp8 18 36 0 1 5 1 0 1 0 6
sp9 1 0 0 0 0 1 1 0 0 8
sp10 18 0 0 0 0 0 0 0 0 38
sp11 15 46 7 0 37 1 0 0 0 14
sp12 7 0 0 0 0 0 0 8 2 0
sp13 3 0 25 4 0 17 1 19 5 6
sp14 4 0 0 0 0 0 0 0 0 0
sp15 2 0 0 0 0 0 0 0 0 1
sp16 1 7 13 1 10 0 0 0 0 0
sp17 1 0 1 0 0 0 0 0 0 0
sp18 2 0 1 0 0 0 0 0 0 1
sp19 4 1 0 1 0 0 0 0 0 1
sp20 1 3 0 1 0 0 0 0 0 0
> phy
Phylogenetic tree with 20 tips and 19 internal nodes.
Tip labels:
sp1, sp2, sp3, sp4, sp5, sp6, ...
Rooted; includes branch lengths.
> trt
trt.1 trt.2
sp1 0.21 10
sp2 0.02 10
sp3 0.78 5
sp4 0.05 8
sp5 0.56 6
sp6 0.28 12
sp7 0.33 1
sp8 0.65 10
sp9 0.23 9
sp10 0.62 7
sp11 0.06 5
sp12 0.30 18
sp13 0.18 10
sp14 0.82 10
sp15 0.64 11
sp16 0.41 16
sp17 0.03 4
sp18 0.42 12
sp19 0.76 16
sp20 0.05 5
>
> # prune out undersampled plots
> spl[,2]=0
> match.spacodi.data(spl) -> sp.plot.new
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
spacodiR
--- call from context ---
reorderspacodiobj(sp.plot, usable.species)
--- call from argument ---
if (class(obj) == "phylo") {
obj.labels = obj$tip.label
if (any(!obj.labels %in% names))
obj = drop.tip(obj, obj.labels[!obj.labels %in% names])
else obj = obj
} else if (check.distmat(obj)) {
obj.labels = rownames(obj)
obj = as.matrix(obj[match(names, obj.labels), match(names,
obj.labels)])
rownames(obj) <- colnames(obj) <- names
} else {
nn = colnames(obj)
obj.labels = rownames(obj)
obj = as.data.frame(obj[match(names, obj.labels), ])
names(obj) = nn
}
--- R stacktrace ---
where 1: reorderspacodiobj(sp.plot, usable.species)
where 2: rownames(sp.plot)
where 3: prune.sp(reorderspacodiobj(sp.plot, usable.species), verbose = verbose)
where 4: match.spacodi.data(spl)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (obj, names)
{
if (class(obj) == "phylo") {
obj.labels = obj$tip.label
if (any(!obj.labels %in% names))
obj = drop.tip(obj, obj.labels[!obj.labels %in% names])
else obj = obj
}
else if (check.distmat(obj)) {
obj.labels = rownames(obj)
obj = as.matrix(obj[match(names, obj.labels), match(names,
obj.labels)])
rownames(obj) <- colnames(obj) <- names
}
else {
nn = colnames(obj)
obj.labels = rownames(obj)
obj = as.data.frame(obj[match(names, obj.labels), ])
names(obj) = nn
}
if (!all(names %in% obj.labels))
warning(paste(paste(names[!names %in% obj.labels], sep = " ",
collapse = " "), "were not found in the supplied object",
sep = " "))
return(obj)
}
<bytecode: 0xb69bf28>
<environment: namespace:spacodiR>
--- function search by body ---
Function reorderspacodiobj in namespace spacodiR has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(obj) == "phylo") { : the condition has length > 1
Calls: match.spacodi.data -> prune.sp -> rownames -> reorderspacodiobj
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.13.0115
Check: examples
Result: ERROR
Running examples in ‘spacodiR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: match.spacodi.data
> ### Title: pruning a tree to match datasets used in SPACoDi
> ### Aliases: match.spacodi.data
>
> ### ** Examples
>
> # load a species-by-plots matrix, along with a tree
> data(sp.example)
> attributes(sp.example)
$names
[1] "spl" "phy" "trt" "dis"
> attach(sp.example)
> spl
plot1 plot2 plot3 plot4 plot5 plot6 plot7 plot8 plot9 plot10
sp1 7 0 0 0 1 0 0 0 0 0
sp2 1 0 0 0 0 3 1 1 0 83
sp3 3 8 1 0 1 0 0 0 0 0
sp4 2 0 0 0 0 0 0 0 0 7
sp5 1 2 0 0 0 0 0 0 0 1
sp6 1 0 0 0 0 0 0 0 0 0
sp7 1 0 0 0 0 0 0 0 0 14
sp8 18 36 0 1 5 1 0 1 0 6
sp9 1 0 0 0 0 1 1 0 0 8
sp10 18 0 0 0 0 0 0 0 0 38
sp11 15 46 7 0 37 1 0 0 0 14
sp12 7 0 0 0 0 0 0 8 2 0
sp13 3 0 25 4 0 17 1 19 5 6
sp14 4 0 0 0 0 0 0 0 0 0
sp15 2 0 0 0 0 0 0 0 0 1
sp16 1 7 13 1 10 0 0 0 0 0
sp17 1 0 1 0 0 0 0 0 0 0
sp18 2 0 1 0 0 0 0 0 0 1
sp19 4 1 0 1 0 0 0 0 0 1
sp20 1 3 0 1 0 0 0 0 0 0
> phy
Phylogenetic tree with 20 tips and 19 internal nodes.
Tip labels:
sp1, sp2, sp3, sp4, sp5, sp6, ...
Rooted; includes branch lengths.
> trt
trt.1 trt.2
sp1 0.21 10
sp2 0.02 10
sp3 0.78 5
sp4 0.05 8
sp5 0.56 6
sp6 0.28 12
sp7 0.33 1
sp8 0.65 10
sp9 0.23 9
sp10 0.62 7
sp11 0.06 5
sp12 0.30 18
sp13 0.18 10
sp14 0.82 10
sp15 0.64 11
sp16 0.41 16
sp17 0.03 4
sp18 0.42 12
sp19 0.76 16
sp20 0.05 5
>
> # prune out undersampled plots
> spl[,2]=0
> match.spacodi.data(spl) -> sp.plot.new
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
spacodiR
--- call from context ---
reorderspacodiobj(sp.plot, usable.species)
--- call from argument ---
if (class(obj) == "phylo") {
obj.labels = obj$tip.label
if (any(!obj.labels %in% names))
obj = drop.tip(obj, obj.labels[!obj.labels %in% names])
else obj = obj
} else if (check.distmat(obj)) {
obj.labels = rownames(obj)
obj = as.matrix(obj[match(names, obj.labels), match(names,
obj.labels)])
rownames(obj) <- colnames(obj) <- names
} else {
nn = colnames(obj)
obj.labels = rownames(obj)
obj = as.data.frame(obj[match(names, obj.labels), ])
names(obj) = nn
}
--- R stacktrace ---
where 1: reorderspacodiobj(sp.plot, usable.species)
where 2: rownames(sp.plot)
where 3: prune.sp(reorderspacodiobj(sp.plot, usable.species), verbose = verbose)
where 4: match.spacodi.data(spl)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (obj, names)
{
if (class(obj) == "phylo") {
obj.labels = obj$tip.label
if (any(!obj.labels %in% names))
obj = drop.tip(obj, obj.labels[!obj.labels %in% names])
else obj = obj
}
else if (check.distmat(obj)) {
obj.labels = rownames(obj)
obj = as.matrix(obj[match(names, obj.labels), match(names,
obj.labels)])
rownames(obj) <- colnames(obj) <- names
}
else {
nn = colnames(obj)
obj.labels = rownames(obj)
obj = as.data.frame(obj[match(names, obj.labels), ])
names(obj) = nn
}
if (!all(names %in% obj.labels))
warning(paste(paste(names[!names %in% obj.labels], sep = " ",
collapse = " "), "were not found in the supplied object",
sep = " "))
return(obj)
}
<bytecode: 0x560d6c036368>
<environment: namespace:spacodiR>
--- function search by body ---
Function reorderspacodiobj in namespace spacodiR has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(obj) == "phylo") { : the condition has length > 1
Calls: match.spacodi.data -> prune.sp -> rownames -> reorderspacodiobj
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.13.0115
Check: compiled code
Result: NOTE
File ‘spacodiR/libs/spacodiR.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.13.0115
Check: examples
Result: ERROR
Running examples in ‘spacodiR-Ex.R’ failed
The error most likely occurred in:
> ### Name: match.spacodi.data
> ### Title: pruning a tree to match datasets used in SPACoDi
> ### Aliases: match.spacodi.data
>
> ### ** Examples
>
> # load a species-by-plots matrix, along with a tree
> data(sp.example)
> attributes(sp.example)
$names
[1] "spl" "phy" "trt" "dis"
> attach(sp.example)
> spl
plot1 plot2 plot3 plot4 plot5 plot6 plot7 plot8 plot9 plot10
sp1 7 0 0 0 1 0 0 0 0 0
sp2 1 0 0 0 0 3 1 1 0 83
sp3 3 8 1 0 1 0 0 0 0 0
sp4 2 0 0 0 0 0 0 0 0 7
sp5 1 2 0 0 0 0 0 0 0 1
sp6 1 0 0 0 0 0 0 0 0 0
sp7 1 0 0 0 0 0 0 0 0 14
sp8 18 36 0 1 5 1 0 1 0 6
sp9 1 0 0 0 0 1 1 0 0 8
sp10 18 0 0 0 0 0 0 0 0 38
sp11 15 46 7 0 37 1 0 0 0 14
sp12 7 0 0 0 0 0 0 8 2 0
sp13 3 0 25 4 0 17 1 19 5 6
sp14 4 0 0 0 0 0 0 0 0 0
sp15 2 0 0 0 0 0 0 0 0 1
sp16 1 7 13 1 10 0 0 0 0 0
sp17 1 0 1 0 0 0 0 0 0 0
sp18 2 0 1 0 0 0 0 0 0 1
sp19 4 1 0 1 0 0 0 0 0 1
sp20 1 3 0 1 0 0 0 0 0 0
> phy
Phylogenetic tree with 20 tips and 19 internal nodes.
Tip labels:
sp1, sp2, sp3, sp4, sp5, sp6, ...
Rooted; includes branch lengths.
> trt
trt.1 trt.2
sp1 0.21 10
sp2 0.02 10
sp3 0.78 5
sp4 0.05 8
sp5 0.56 6
sp6 0.28 12
sp7 0.33 1
sp8 0.65 10
sp9 0.23 9
sp10 0.62 7
sp11 0.06 5
sp12 0.30 18
sp13 0.18 10
sp14 0.82 10
sp15 0.64 11
sp16 0.41 16
sp17 0.03 4
sp18 0.42 12
sp19 0.76 16
sp20 0.05 5
>
> # prune out undersampled plots
> spl[,2]=0
> match.spacodi.data(spl) -> sp.plot.new
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
spacodiR
--- call from context ---
reorderspacodiobj(sp.plot, usable.species)
--- call from argument ---
if (class(obj) == "phylo") {
obj.labels = obj$tip.label
if (any(!obj.labels %in% names))
obj = drop.tip(obj, obj.labels[!obj.labels %in% names])
else obj = obj
} else if (check.distmat(obj)) {
obj.labels = rownames(obj)
obj = as.matrix(obj[match(names, obj.labels), match(names,
obj.labels)])
rownames(obj) <- colnames(obj) <- names
} else {
nn = colnames(obj)
obj.labels = rownames(obj)
obj = as.data.frame(obj[match(names, obj.labels), ])
names(obj) = nn
}
--- R stacktrace ---
where 1: reorderspacodiobj(sp.plot, usable.species)
where 2: rownames(sp.plot)
where 3: prune.sp(reorderspacodiobj(sp.plot, usable.species), verbose = verbose)
where 4: match.spacodi.data(spl)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (obj, names)
{
if (class(obj) == "phylo") {
obj.labels = obj$tip.label
if (any(!obj.labels %in% names))
obj = drop.tip(obj, obj.labels[!obj.labels %in% names])
else obj = obj
}
else if (check.distmat(obj)) {
obj.labels = rownames(obj)
obj = as.matrix(obj[match(names, obj.labels), match(names,
obj.labels)])
rownames(obj) <- colnames(obj) <- names
}
else {
nn = colnames(obj)
obj.labels = rownames(obj)
obj = as.data.frame(obj[match(names, obj.labels), ])
names(obj) = nn
}
if (!all(names %in% obj.labels))
warning(paste(paste(names[!names %in% obj.labels], sep = " ",
collapse = " "), "were not found in the supplied object",
sep = " "))
return(obj)
}
<bytecode: 0x9e25280>
<environment: namespace:spacodiR>
--- function search by body ---
Function reorderspacodiobj in namespace spacodiR has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(obj) == "phylo") { : the condition has length > 1
Calls: match.spacodi.data -> prune.sp -> rownames -> reorderspacodiobj
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.13.0115
Check: examples
Result: ERROR
Running examples in ‘spacodiR-Ex.R’ failed
The error most likely occurred in:
> ### Name: match.spacodi.data
> ### Title: pruning a tree to match datasets used in SPACoDi
> ### Aliases: match.spacodi.data
>
> ### ** Examples
>
> # load a species-by-plots matrix, along with a tree
> data(sp.example)
> attributes(sp.example)
$names
[1] "spl" "phy" "trt" "dis"
> attach(sp.example)
> spl
plot1 plot2 plot3 plot4 plot5 plot6 plot7 plot8 plot9 plot10
sp1 7 0 0 0 1 0 0 0 0 0
sp2 1 0 0 0 0 3 1 1 0 83
sp3 3 8 1 0 1 0 0 0 0 0
sp4 2 0 0 0 0 0 0 0 0 7
sp5 1 2 0 0 0 0 0 0 0 1
sp6 1 0 0 0 0 0 0 0 0 0
sp7 1 0 0 0 0 0 0 0 0 14
sp8 18 36 0 1 5 1 0 1 0 6
sp9 1 0 0 0 0 1 1 0 0 8
sp10 18 0 0 0 0 0 0 0 0 38
sp11 15 46 7 0 37 1 0 0 0 14
sp12 7 0 0 0 0 0 0 8 2 0
sp13 3 0 25 4 0 17 1 19 5 6
sp14 4 0 0 0 0 0 0 0 0 0
sp15 2 0 0 0 0 0 0 0 0 1
sp16 1 7 13 1 10 0 0 0 0 0
sp17 1 0 1 0 0 0 0 0 0 0
sp18 2 0 1 0 0 0 0 0 0 1
sp19 4 1 0 1 0 0 0 0 0 1
sp20 1 3 0 1 0 0 0 0 0 0
> phy
Phylogenetic tree with 20 tips and 19 internal nodes.
Tip labels:
sp1, sp2, sp3, sp4, sp5, sp6, ...
Rooted; includes branch lengths.
> trt
trt.1 trt.2
sp1 0.21 10
sp2 0.02 10
sp3 0.78 5
sp4 0.05 8
sp5 0.56 6
sp6 0.28 12
sp7 0.33 1
sp8 0.65 10
sp9 0.23 9
sp10 0.62 7
sp11 0.06 5
sp12 0.30 18
sp13 0.18 10
sp14 0.82 10
sp15 0.64 11
sp16 0.41 16
sp17 0.03 4
sp18 0.42 12
sp19 0.76 16
sp20 0.05 5
>
> # prune out undersampled plots
> spl[,2]=0
> match.spacodi.data(spl) -> sp.plot.new
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
spacodiR
--- call from context ---
reorderspacodiobj(sp.plot, usable.species)
--- call from argument ---
if (class(obj) == "phylo") {
obj.labels = obj$tip.label
if (any(!obj.labels %in% names))
obj = drop.tip(obj, obj.labels[!obj.labels %in% names])
else obj = obj
} else if (check.distmat(obj)) {
obj.labels = rownames(obj)
obj = as.matrix(obj[match(names, obj.labels), match(names,
obj.labels)])
rownames(obj) <- colnames(obj) <- names
} else {
nn = colnames(obj)
obj.labels = rownames(obj)
obj = as.data.frame(obj[match(names, obj.labels), ])
names(obj) = nn
}
--- R stacktrace ---
where 1: reorderspacodiobj(sp.plot, usable.species)
where 2: rownames(sp.plot)
where 3: prune.sp(reorderspacodiobj(sp.plot, usable.species), verbose = verbose)
where 4: match.spacodi.data(spl)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (obj, names)
{
if (class(obj) == "phylo") {
obj.labels = obj$tip.label
if (any(!obj.labels %in% names))
obj = drop.tip(obj, obj.labels[!obj.labels %in% names])
else obj = obj
}
else if (check.distmat(obj)) {
obj.labels = rownames(obj)
obj = as.matrix(obj[match(names, obj.labels), match(names,
obj.labels)])
rownames(obj) <- colnames(obj) <- names
}
else {
nn = colnames(obj)
obj.labels = rownames(obj)
obj = as.data.frame(obj[match(names, obj.labels), ])
names(obj) = nn
}
if (!all(names %in% obj.labels))
warning(paste(paste(names[!names %in% obj.labels], sep = " ",
collapse = " "), "were not found in the supplied object",
sep = " "))
return(obj)
}
<bytecode: 0xae83a48>
<environment: namespace:spacodiR>
--- function search by body ---
Function reorderspacodiobj in namespace spacodiR has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(obj) == "phylo") { : the condition has length > 1
Calls: match.spacodi.data -> prune.sp -> rownames -> reorderspacodiobj
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.13.0115
Check: R code for possible problems
Result: NOTE
add.transparency: no visible global function definition for 'col2rgb'
add.transparency: no visible global function definition for 'rgb'
as.phylocom: no visible global function definition for 'write.table'
as.picante: no visible global function definition for 'write.table'
as.spacodi: no visible global function definition for 'write.table'
cophen: no visible global function definition for 'Ntip'
get.descendants.of.node: no visible global function definition for
'Ntip'
phy.deresolve: no visible global function definition for
'branching.times'
phy.deresolve: no visible global function definition for 'Ntip'
phy.dotplot: no visible global function definition for 'par'
phy.dotplot: no visible global function definition for 'pdf'
phy.dotplot: no visible global function definition for 'layout'
phy.dotplot: no visible global function definition for 'plot'
phy.dotplot: no visible global function definition for 'tiplabels'
phy.dotplot: no visible global function definition for 'legend'
phy.dotplot: no visible global function definition for 'dev.off'
phy.dotplot: no visible global function definition for 'dev.new'
phy.nodetimes: no visible global function definition for 'Ntip'
phy.nodetimes: no visible global function definition for
'branching.times'
reorderspacodiobj: no visible global function definition for 'drop.tip'
resamp.1a: no visible global function definition for 'runif'
resamp.3t: no visible global function definition for 'runif'
resamp.phy: no visible global function definition for 'Ntip'
resamp.phy: no visible global function definition for 'branching.times'
spacodi.all.nodes: no visible global function definition for 'subtrees'
spacodi.all.nodes: no visible global function definition for
'branching.times'
spacodi.calc: no visible global function definition for 'dist'
spacodi.calc : <anonymous>: no visible global function definition for
'dist'
spacodi.exp.nodes: no visible global function definition for 'subtrees'
spacodi.permutplot: no visible global function definition for 'pdf'
spacodi.permutplot: no visible global function definition for 'plot'
spacodi.permutplot: no visible global function definition for 'points'
spacodi.permutplot: no visible global function definition for 'lines'
spacodi.permutplot: no visible global function definition for
'smooth.spline'
spacodi.permutplot: no visible global function definition for 'legend'
spacodi.permutplot: no visible global function definition for 'dev.off'
spacodi.treeplot: no visible global function definition for 'pdf'
spacodi.treeplot: no visible global function definition for
'diverge_hcl'
spacodi.treeplot: no visible global function definition for 'plot'
spacodi.treeplot: no visible global function definition for
'nodelabels'
spacodi.treeplot: no visible global function definition for 'legend'
spacodi.treeplot: no visible global function definition for 'title'
spacodi.treeplot: no visible global function definition for 'dev.off'
textxy: no visible global function definition for 'text'
write.spacodi.data: no visible global function definition for
'write.table'
Undefined global functions or variables:
Ntip branching.times col2rgb dev.new dev.off dist diverge_hcl
drop.tip layout legend lines nodelabels par pdf plot points rgb runif
smooth.spline subtrees text tiplabels title write.table
Consider adding
importFrom("grDevices", "col2rgb", "dev.new", "dev.off", "pdf", "rgb")
importFrom("graphics", "layout", "legend", "lines", "par", "plot",
"points", "text", "title")
importFrom("stats", "dist", "runif", "smooth.spline")
importFrom("utils", "write.table")
to your NAMESPACE file.
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, 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: 0.13.0115
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘spacodi.formatted.txt’
Flavor: r-patched-solaris-x86