Last updated on 2020-02-19 10:49:02 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0 | 1.82 | 17.61 | 19.43 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0 | 1.48 | 14.13 | 15.61 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0 | 24.47 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0 | 23.70 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.0 | 5.00 | 28.00 | 33.00 | NOTE | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.0 | 8.00 | 41.00 | 49.00 | NOTE | |
| r-patched-linux-x86_64 | 1.0 | 1.24 | 15.55 | 16.79 | NOTE | |
| r-patched-solaris-x86 | 1.0 | 33.70 | NOTE | |||
| r-release-linux-x86_64 | 1.0 | 1.22 | 15.64 | 16.86 | NOTE | |
| r-release-windows-ix86+x86_64 | 1.0 | 4.00 | 38.00 | 42.00 | NOTE | |
| r-release-osx-x86_64 | 1.0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0 | 2.00 | 27.00 | 29.00 | NOTE | |
| r-oldrel-osx-x86_64 | 1.0 | NOTE |
Version: 1.0
Check: R code for possible problems
Result: NOTE
ParentOffspring: no visible global function definition for 'axis'
ParentOffspring: no visible global function definition for 'abline'
ParentOffspring: no visible global function definition for 'title'
ParentOffspring: no visible global function definition for 'box'
Undefined global functions or variables:
abline axis box title
Consider adding
importFrom("graphics", "abline", "axis", "box", "title")
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: 1.0
Check: examples
Result: ERROR
Running examples in 'ParentOffspring-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ParentOffspring
> ### Title: Conduct the Parent-Offspring Test Using Monomorphic SNP Markers
> ### Aliases: ParentOffspring
> ### Keywords: parent offspring test monomorphic SNP markers
>
> ### ** Examples
>
>
> # a very simple example
>
> genotypeMatrix = matrix(
+ c("GG", "GG", "GG", "CG", "CG", "GG",
+ "AA", "AA", "AA", "--", "AA", "AA",
+ "AA", "AA", "GG", "AA", "AA", "AA",
+ "GG", "AA", "GG", "GG", "GG", "GG"),
+ byrow=TRUE,
+ nrow=4,
+ ncol=6)
> # Compute and plot the parent-offspring similarity for each offspring
> ParentOffspring(genotypeMatrix)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
ParentOffspring
--- call from context ---
ParentOffspring(genotypeMatrix)
--- call from argument ---
if (class(genoMat) == "data.frame") genoMat = as.matrix(genoMat)
--- R stacktrace ---
where 1: ParentOffspring(genotypeMatrix)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (genoMat, plot = TRUE)
{
if (class(genoMat) == "data.frame")
genoMat = as.matrix(genoMat)
dimension = dim(genoMat)
if (dimension[1] < 1)
stop("the input genoMat is empty")
if (dimension[2] < 3)
stop("the input genoMat should have at least 3 columns")
aa = unlist(lapply(unlist(genoMat), is.character))
if (min(aa) == 0)
stop("the input genoMat has noncharacter values")
if (min(nchar(unlist(genoMat)) == 2) == 0)
stop("the input genoMat has values which are not 2-letter strings")
geno <- genoMat
geno <- geno[(geno[, 1]) == (geno[, 2]), ]
geno <- geno[(substr(geno[, 1], 1, 1)) == (substr(geno[,
1], 2, 2)), ]
geno <- geno[(geno[, 1]) != "--", ]
dimension <- dim(geno)
markersN <- dimension[1]
offspringN <- dimension[2] - 2
if (markersN < 1)
stop("No monomorphic markers can be used")
parent <- geno[, 1]
offspring <- geno[, -(1:2)]
markersValidN <- rep(0, offspringN)
similarityMat <- matrix(0, markersN, offspringN)
for (i in 1:offspringN) {
similarityMat[, i] <- (substr(parent, 1, 1) == substr(offspring[,
i], 1, 1)) + (substr(parent, 1, 1) == substr(offspring[,
i], 2, 2))
for (j in 1:markersN) {
if ((substr(offspring[j, i], 1, 1) == "-") || (substr(offspring[j,
i], 2, 2) == "-")) {
similarityMat[j, i] <- NA
}
}
markersValidN[i] <- markersN - sum(is.na(similarityMat[,
i]))
}
similarityMat <- similarityMat/2
similarity <- round(colMeans(similarityMat, na.rm = T), 2)
if (plot == TRUE) {
plot(1:offspringN, sort(similarity, decreasing = T),
pch = "*", cex = 2, col = "red", ylim = c(0.5, 1),
xlab = "offspring sorted by similarity", ylab = "similarity",
axes = FALSE)
axis(side = 1, at = 1:offspringN)
axis(side = 2, at = c(round((5:10)/10, 1), 0.95, 0.99))
abline(h = c(0.9, 0.95, 0.99), lty = 2, col = "blue",
lwd = 2)
title("Similarity to the Parents")
box()
}
return(similarity)
}
<bytecode: 0x1d92158>
<environment: namespace:ParentOffspring>
--- function search by body ---
Function ParentOffspring in namespace ParentOffspring has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(genoMat) == "data.frame") genoMat = as.matrix(genoMat) :
the condition has length > 1
Calls: ParentOffspring
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0
Check: examples
Result: ERROR
Running examples in ‘ParentOffspring-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ParentOffspring
> ### Title: Conduct the Parent-Offspring Test Using Monomorphic SNP Markers
> ### Aliases: ParentOffspring
> ### Keywords: parent offspring test monomorphic SNP markers
>
> ### ** Examples
>
>
> # a very simple example
>
> genotypeMatrix = matrix(
+ c("GG", "GG", "GG", "CG", "CG", "GG",
+ "AA", "AA", "AA", "--", "AA", "AA",
+ "AA", "AA", "GG", "AA", "AA", "AA",
+ "GG", "AA", "GG", "GG", "GG", "GG"),
+ byrow=TRUE,
+ nrow=4,
+ ncol=6)
> # Compute and plot the parent-offspring similarity for each offspring
> ParentOffspring(genotypeMatrix)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
ParentOffspring
--- call from context ---
ParentOffspring(genotypeMatrix)
--- call from argument ---
if (class(genoMat) == "data.frame") genoMat = as.matrix(genoMat)
--- R stacktrace ---
where 1: ParentOffspring(genotypeMatrix)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (genoMat, plot = TRUE)
{
if (class(genoMat) == "data.frame")
genoMat = as.matrix(genoMat)
dimension = dim(genoMat)
if (dimension[1] < 1)
stop("the input genoMat is empty")
if (dimension[2] < 3)
stop("the input genoMat should have at least 3 columns")
aa = unlist(lapply(unlist(genoMat), is.character))
if (min(aa) == 0)
stop("the input genoMat has noncharacter values")
if (min(nchar(unlist(genoMat)) == 2) == 0)
stop("the input genoMat has values which are not 2-letter strings")
geno <- genoMat
geno <- geno[(geno[, 1]) == (geno[, 2]), ]
geno <- geno[(substr(geno[, 1], 1, 1)) == (substr(geno[,
1], 2, 2)), ]
geno <- geno[(geno[, 1]) != "--", ]
dimension <- dim(geno)
markersN <- dimension[1]
offspringN <- dimension[2] - 2
if (markersN < 1)
stop("No monomorphic markers can be used")
parent <- geno[, 1]
offspring <- geno[, -(1:2)]
markersValidN <- rep(0, offspringN)
similarityMat <- matrix(0, markersN, offspringN)
for (i in 1:offspringN) {
similarityMat[, i] <- (substr(parent, 1, 1) == substr(offspring[,
i], 1, 1)) + (substr(parent, 1, 1) == substr(offspring[,
i], 2, 2))
for (j in 1:markersN) {
if ((substr(offspring[j, i], 1, 1) == "-") || (substr(offspring[j,
i], 2, 2) == "-")) {
similarityMat[j, i] <- NA
}
}
markersValidN[i] <- markersN - sum(is.na(similarityMat[,
i]))
}
similarityMat <- similarityMat/2
similarity <- round(colMeans(similarityMat, na.rm = T), 2)
if (plot == TRUE) {
plot(1:offspringN, sort(similarity, decreasing = T),
pch = "*", cex = 2, col = "red", ylim = c(0.5, 1),
xlab = "offspring sorted by similarity", ylab = "similarity",
axes = FALSE)
axis(side = 1, at = 1:offspringN)
axis(side = 2, at = c(round((5:10)/10, 1), 0.95, 0.99))
abline(h = c(0.9, 0.95, 0.99), lty = 2, col = "blue",
lwd = 2)
title("Similarity to the Parents")
box()
}
return(similarity)
}
<bytecode: 0x56335b4c40a8>
<environment: namespace:ParentOffspring>
--- function search by body ---
Function ParentOffspring in namespace ParentOffspring has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(genoMat) == "data.frame") genoMat = as.matrix(genoMat) :
the condition has length > 1
Calls: ParentOffspring
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0
Check: examples
Result: ERROR
Running examples in ‘ParentOffspring-Ex.R’ failed
The error most likely occurred in:
> ### Name: ParentOffspring
> ### Title: Conduct the Parent-Offspring Test Using Monomorphic SNP Markers
> ### Aliases: ParentOffspring
> ### Keywords: parent offspring test monomorphic SNP markers
>
> ### ** Examples
>
>
> # a very simple example
>
> genotypeMatrix = matrix(
+ c("GG", "GG", "GG", "CG", "CG", "GG",
+ "AA", "AA", "AA", "--", "AA", "AA",
+ "AA", "AA", "GG", "AA", "AA", "AA",
+ "GG", "AA", "GG", "GG", "GG", "GG"),
+ byrow=TRUE,
+ nrow=4,
+ ncol=6)
> # Compute and plot the parent-offspring similarity for each offspring
> ParentOffspring(genotypeMatrix)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
ParentOffspring
--- call from context ---
ParentOffspring(genotypeMatrix)
--- call from argument ---
if (class(genoMat) == "data.frame") genoMat = as.matrix(genoMat)
--- R stacktrace ---
where 1: ParentOffspring(genotypeMatrix)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (genoMat, plot = TRUE)
{
if (class(genoMat) == "data.frame")
genoMat = as.matrix(genoMat)
dimension = dim(genoMat)
if (dimension[1] < 1)
stop("the input genoMat is empty")
if (dimension[2] < 3)
stop("the input genoMat should have at least 3 columns")
aa = unlist(lapply(unlist(genoMat), is.character))
if (min(aa) == 0)
stop("the input genoMat has noncharacter values")
if (min(nchar(unlist(genoMat)) == 2) == 0)
stop("the input genoMat has values which are not 2-letter strings")
geno <- genoMat
geno <- geno[(geno[, 1]) == (geno[, 2]), ]
geno <- geno[(substr(geno[, 1], 1, 1)) == (substr(geno[,
1], 2, 2)), ]
geno <- geno[(geno[, 1]) != "--", ]
dimension <- dim(geno)
markersN <- dimension[1]
offspringN <- dimension[2] - 2
if (markersN < 1)
stop("No monomorphic markers can be used")
parent <- geno[, 1]
offspring <- geno[, -(1:2)]
markersValidN <- rep(0, offspringN)
similarityMat <- matrix(0, markersN, offspringN)
for (i in 1:offspringN) {
similarityMat[, i] <- (substr(parent, 1, 1) == substr(offspring[,
i], 1, 1)) + (substr(parent, 1, 1) == substr(offspring[,
i], 2, 2))
for (j in 1:markersN) {
if ((substr(offspring[j, i], 1, 1) == "-") || (substr(offspring[j,
i], 2, 2) == "-")) {
similarityMat[j, i] <- NA
}
}
markersValidN[i] <- markersN - sum(is.na(similarityMat[,
i]))
}
similarityMat <- similarityMat/2
similarity <- round(colMeans(similarityMat, na.rm = T), 2)
if (plot == TRUE) {
plot(1:offspringN, sort(similarity, decreasing = T),
pch = "*", cex = 2, col = "red", ylim = c(0.5, 1),
xlab = "offspring sorted by similarity", ylab = "similarity",
axes = FALSE)
axis(side = 1, at = 1:offspringN)
axis(side = 2, at = c(round((5:10)/10, 1), 0.95, 0.99))
abline(h = c(0.9, 0.95, 0.99), lty = 2, col = "blue",
lwd = 2)
title("Similarity to the Parents")
box()
}
return(similarity)
}
<bytecode: 0x3134818>
<environment: namespace:ParentOffspring>
--- function search by body ---
Function ParentOffspring in namespace ParentOffspring has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(genoMat) == "data.frame") genoMat = as.matrix(genoMat) :
the condition has length > 1
Calls: ParentOffspring
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0
Check: examples
Result: ERROR
Running examples in ‘ParentOffspring-Ex.R’ failed
The error most likely occurred in:
> ### Name: ParentOffspring
> ### Title: Conduct the Parent-Offspring Test Using Monomorphic SNP Markers
> ### Aliases: ParentOffspring
> ### Keywords: parent offspring test monomorphic SNP markers
>
> ### ** Examples
>
>
> # a very simple example
>
> genotypeMatrix = matrix(
+ c("GG", "GG", "GG", "CG", "CG", "GG",
+ "AA", "AA", "AA", "--", "AA", "AA",
+ "AA", "AA", "GG", "AA", "AA", "AA",
+ "GG", "AA", "GG", "GG", "GG", "GG"),
+ byrow=TRUE,
+ nrow=4,
+ ncol=6)
> # Compute and plot the parent-offspring similarity for each offspring
> ParentOffspring(genotypeMatrix)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
ParentOffspring
--- call from context ---
ParentOffspring(genotypeMatrix)
--- call from argument ---
if (class(genoMat) == "data.frame") genoMat = as.matrix(genoMat)
--- R stacktrace ---
where 1: ParentOffspring(genotypeMatrix)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (genoMat, plot = TRUE)
{
if (class(genoMat) == "data.frame")
genoMat = as.matrix(genoMat)
dimension = dim(genoMat)
if (dimension[1] < 1)
stop("the input genoMat is empty")
if (dimension[2] < 3)
stop("the input genoMat should have at least 3 columns")
aa = unlist(lapply(unlist(genoMat), is.character))
if (min(aa) == 0)
stop("the input genoMat has noncharacter values")
if (min(nchar(unlist(genoMat)) == 2) == 0)
stop("the input genoMat has values which are not 2-letter strings")
geno <- genoMat
geno <- geno[(geno[, 1]) == (geno[, 2]), ]
geno <- geno[(substr(geno[, 1], 1, 1)) == (substr(geno[,
1], 2, 2)), ]
geno <- geno[(geno[, 1]) != "--", ]
dimension <- dim(geno)
markersN <- dimension[1]
offspringN <- dimension[2] - 2
if (markersN < 1)
stop("No monomorphic markers can be used")
parent <- geno[, 1]
offspring <- geno[, -(1:2)]
markersValidN <- rep(0, offspringN)
similarityMat <- matrix(0, markersN, offspringN)
for (i in 1:offspringN) {
similarityMat[, i] <- (substr(parent, 1, 1) == substr(offspring[,
i], 1, 1)) + (substr(parent, 1, 1) == substr(offspring[,
i], 2, 2))
for (j in 1:markersN) {
if ((substr(offspring[j, i], 1, 1) == "-") || (substr(offspring[j,
i], 2, 2) == "-")) {
similarityMat[j, i] <- NA
}
}
markersValidN[i] <- markersN - sum(is.na(similarityMat[,
i]))
}
similarityMat <- similarityMat/2
similarity <- round(colMeans(similarityMat, na.rm = T), 2)
if (plot == TRUE) {
plot(1:offspringN, sort(similarity, decreasing = T),
pch = "*", cex = 2, col = "red", ylim = c(0.5, 1),
xlab = "offspring sorted by similarity", ylab = "similarity",
axes = FALSE)
axis(side = 1, at = 1:offspringN)
axis(side = 2, at = c(round((5:10)/10, 1), 0.95, 0.99))
abline(h = c(0.9, 0.95, 0.99), lty = 2, col = "blue",
lwd = 2)
title("Similarity to the Parents")
box()
}
return(similarity)
}
<bytecode: 0x299c9b0>
<environment: namespace:ParentOffspring>
--- function search by body ---
Function ParentOffspring in namespace ParentOffspring has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(genoMat) == "data.frame") genoMat = as.matrix(genoMat) :
the condition has length > 1
Calls: ParentOffspring
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc