Last updated on 2020-03-07 11:48:28 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.6 | 14.26 | 91.30 | 105.56 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.6 | 13.69 | 71.76 | 85.45 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.6 | 134.04 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.6 | 136.35 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.0.6 | 45.00 | 179.00 | 224.00 | NOTE | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.0.6 | 30.00 | 129.00 | 159.00 | NOTE | |
| r-patched-linux-x86_64 | 1.0.6 | 12.81 | 77.41 | 90.22 | NOTE | |
| r-patched-solaris-x86 | 1.0.6 | 191.90 | NOTE | |||
| r-release-linux-x86_64 | 1.0.6 | 13.97 | 77.71 | 91.68 | NOTE | |
| r-release-windows-ix86+x86_64 | 1.0.6 | 27.00 | 137.00 | 164.00 | NOTE | |
| r-release-osx-x86_64 | 1.0.6 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.6 | 18.00 | 106.00 | 124.00 | NOTE | |
| r-oldrel-osx-x86_64 | 1.0.6 | NOTE |
Version: 1.0.6
Check: package dependencies
Result: NOTE
Depends: includes the non-default packages:
'biwt', 'cairoDevice', 'fBasics', 'gplots', 'gWidgets',
'gWidgetsRGtk2', 'minerva', 'parmigene', 'stringr', 'snowfall'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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
Version: 1.0.6
Check: dependencies in R code
Result: NOTE
'library' or 'require' calls to packages already attached by Depends:
'grDevices' 'snowfall'
Please remove these calls from your code.
'library' or 'require' call to 'ctc' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'biwt' 'cairoDevice' 'fBasics' 'gWidgets' 'gWidgetsRGtk2' 'gplots'
'minerva' 'parmigene' 'snowfall' 'stringr'
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: 1.0.6
Check: R code for possible problems
Result: NOTE
.cor_all: no visible global function definition for 'as.big.matrix'
adjacencymatrix: no visible global function definition for
'as.big.matrix'
adjacencymatrix: no visible global function definition for 'mine'
adjacencymatrix: no visible global function definition for
'knnmi.cross'
adjacencymatrix: no visible global function definition for 'knnmi.all'
cor.matrix: no visible global function definition for 'sfInit'
cor.matrix: no visible global function definition for 'sfCpus'
cor.matrix: no visible global function definition for 'sfApply'
cor.matrix: no visible global function definition for 'sfStop'
cor.pair : getcor: no visible global function definition for 'cor.test'
cor.pair : getcor: no visible global function definition for 'biwt.cor'
cor.pair: no visible global function definition for 'runif'
gcc.dist: no visible global function definition for 'as.dist'
gcc.hclust: no visible global function definition for 'hclust'
gcc.heatmap: no visible global function definition for 'par'
gcc.heatmap: no visible global function definition for 'median'
gcc.heatmap: no visible global function definition for
'order.dendrogram'
gcc.heatmap: no visible global function definition for 'as.dendrogram'
gcc.heatmap: no visible global function definition for 'reorder'
gcc.heatmap: no visible binding for global variable 'sd'
gcc.heatmap: no visible global function definition for 'quantile'
gcc.heatmap: no visible global function definition for
'colorRampPalette'
gcc.heatmap: no visible global function definition for 'layout'
gcc.heatmap: no visible global function definition for 'image'
gcc.heatmap: no visible global function definition for 'invalid'
gcc.heatmap: no visible global function definition for 'axis'
gcc.heatmap: no visible global function definition for 'mtext'
gcc.heatmap: no visible global function definition for 'rect'
gcc.heatmap: no visible global function definition for 'abline'
gcc.heatmap: no visible global function definition for 'lines'
gcc.heatmap: no visible global function definition for 'text'
gcc.heatmap: no visible global function definition for 'plot'
gcc.heatmap: no visible global function definition for 'plot.new'
gcc.heatmap: no visible global function definition for 'title'
gcc.heatmap: no visible global function definition for 'density'
gcc.heatmap: no visible global function definition for 'hist'
gcc.tsheatmap: no visible global function definition for 'median'
gcc.tsheatmap: no visible global function definition for
'as.dendrogram'
gcc.tsheatmap: no visible global function definition for 'reorder'
gcc.tsheatmap: no visible global function definition for
'order.dendrogram'
gcc.tsheatmap: no visible global function definition for 'rainbow'
gcc.tsheatmap: no visible binding for global variable 'sd'
gcc.tsheatmap: no visible global function definition for 'quantile'
gcc.tsheatmap: no visible global function definition for
'install.packages'
gcc.tsheatmap: no visible global function definition for
'colorRampPalette'
gcc.tsheatmap: no visible global function definition for 'par'
gcc.tsheatmap: no visible global function definition for 'layout'
gcc.tsheatmap: no visible global function definition for 'image'
gcc.tsheatmap: no visible global function definition for 'axis'
gcc.tsheatmap: no visible global function definition for 'mtext'
rsgcc.gui : coverDecToHex: no visible global function definition for
'.dec.to.hex'
rsgcc.gui : coverDecToHex: no visible global function definition for
'str_length'
rsgcc.gui : coverDecToHex: no visible global function definition for
'str_sub'
rsgcc.gui : fileChoose: no visible global function definition for
'gfile'
rsgcc.gui : fileChoose: no visible binding for global variable 'tail'
rsgcc.gui : fileChoose: no visible global function definition for
'read.table'
rsgcc.gui : fileChoose: no visible global function definition for
'str_sub'
rsgcc.gui : fileChoose: no visible global function definition for
'str_length'
rsgcc.gui : fileChoose: no visible global function definition for
'read.csv'
rsgcc.gui : visData: no visible global function definition for 'svalue'
rsgcc.gui : visData: no visible global function definition for
'gwindow'
rsgcc.gui : visData: no visible global function definition for 'ggroup'
rsgcc.gui : visData: no visible global function definition for 'gtable'
rsgcc.gui : updateHeatmapMax: no visible global function definition for
'svalue'
rsgcc.gui : updateHeatmapMean: no visible global function definition
for 'svalue'
rsgcc.gui : updateHeatmapMin: no visible global function definition for
'svalue'
rsgcc.gui : saveData: no visible global function definition for 'pdf'
rsgcc.gui : saveData: no visible global function definition for
'dev.off'
rsgcc.gui : saveData: no visible global function definition for
'write.table'
rsgcc.gui : saveData: no visible global function definition for 'r2atr'
rsgcc.gui : saveData: no visible global function definition for 'r2gtr'
rsgcc.gui : saveData: no visible global function definition for 'r2cdt'
rsgcc.gui: no visible global function definition for 'gwindow'
rsgcc.gui: no visible global function definition for 'ggroup'
rsgcc.gui: no visible global function definition for 'gframe'
rsgcc.gui: no visible global function definition for 'gbutton'
rsgcc.gui: no visible global function definition for 'gcheckbox'
rsgcc.gui : <anonymous>: no visible global function definition for
'svalue'
rsgcc.gui: no visible global function definition for 'gedit'
rsgcc.gui: no visible global function definition for 'add'
rsgcc.gui: no visible global function definition for 'gradio'
rsgcc.gui: no visible global function definition for 'gcombobox'
rsgcc.gui: no visible global function definition for 'gslider'
rsgcc.gui: no visible global function definition for 'ggraphics'
uniqueTissues: no visible binding for global variable 'tail'
uniqueTissues: no visible global function definition for 'str_sub'
Undefined global functions or variables:
.dec.to.hex abline add as.big.matrix as.dendrogram as.dist axis
biwt.cor colorRampPalette cor.test density dev.off gbutton gcheckbox
gcombobox gedit gfile gframe ggraphics ggroup gradio gslider gtable
gwindow hclust hist image install.packages invalid knnmi.all
knnmi.cross layout lines median mine mtext order.dendrogram par pdf
plot plot.new quantile r2atr r2cdt r2gtr rainbow read.csv read.table
rect reorder runif sd sfApply sfCpus sfInit sfStop str_length str_sub
svalue tail text title write.table
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
"rainbow")
importFrom("graphics", "abline", "axis", "hist", "image", "layout",
"lines", "mtext", "par", "plot", "plot.new", "rect", "text",
"title")
importFrom("stats", "as.dendrogram", "as.dist", "cor.test", "density",
"hclust", "median", "order.dendrogram", "quantile",
"reorder", "runif", "sd")
importFrom("utils", "install.packages", "read.csv", "read.table",
"tail", "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-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: 1.0.6
Check: compiled code
Result: NOTE
File 'rsgcc/libs/rsgcc.so':
Found 'rand_r', possibly from 'rand_r' (C)
Object: 'points.o'
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64
Version: 1.0.6
Check: examples
Result: ERROR
Running examples in 'rsgcc-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cor.pair
> ### Title: compute the correlation between two genes
> ### Aliases: cor.pair gcc.cor.pair gcc.corpair
> ### Keywords: correlation
>
> ### ** Examples
>
>
> data(rsgcc) #load the sample data in rsgcc package
> x <- rnaseq[1:4,] #construct a GEMatrix with the RNA-Seq data of the first four genes
>
> #compute correlation between the 1st and 4th genes
> corpair <- cor.pair(c(1,4), GEMatrix = x, rowORcol = "row",
+ cormethod = "GCC", pernum = 0,
+ sigmethod = "two.sided")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
rsgcc
--- call from context ---
cor.pair(c(1, 4), GEMatrix = x, rowORcol = "row", cormethod = "GCC",
pernum = 0, sigmethod = "two.sided")
--- call from argument ---
if (class(GEMatrix) != "matrix") {
stop("Error: GEMatrix should be a numeric data matrix")
}
--- R stacktrace ---
where 1: cor.pair(c(1, 4), GEMatrix = x, rowORcol = "row", cormethod = "GCC",
pernum = 0, sigmethod = "two.sided")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (idxvec, GEMatrix, rowORcol = c("row", "col"), cormethod = c("GCC",
"PCC", "SCC", "KCC", "BiWt"), pernum = 0, sigmethod = c("two.sided",
"one.sided"))
{
onegcc <- function(x, y) {
getrank <- function(datamatrix) {
if (dim(datamatrix)[1] != 2) {
stop("Error: the row num of datamatrix must be 2")
}
OrderIndex <- order(datamatrix[1, ], decreasing = FALSE)
SortGenePair <- datamatrix[, OrderIndex]
Sort2By1 <- SortGenePair[2, ]
return(list(Sort2By1 = Sort2By1, Sort2By2 = sort(datamatrix[2,
], decreasing = FALSE)))
}
gcc <- function(weightvec, vectsort, vectselfsort) {
Sum1 <- sum(weightvec * vectsort)
Sum2 <- sum(weightvec * vectselfsort)
if (Sum2 == 0) {
cat("\n", x, "\n", y, "\n")
cat("Warning: the Denominator is ZRRO, the value of one variable is consistent.")
gcccor <- 0
}
else {
gcccor <- Sum1/Sum2
}
return(gcccor)
}
Length <- length(x)
Wt <- t(2 * seq(1, Length, by = 1) - Length - 1)
GenePairXY <- t(matrix(c(x, y), ncol = 2))
SortYlist <- getrank(GenePairXY)
gcc.rankx <- gcc(Wt, SortYlist$Sort2By1, SortYlist$Sort2By2)
return(gcc.rankx)
}
if (!is.vector(idxvec) | length(idxvec) != 2) {
stop("Error: idxvec must be a vector with two elements indicating the indexs(rows) in GEMatrix")
}
if (class(GEMatrix) != "matrix") {
stop("Error: GEMatrix should be a numeric data matrix")
}
if (rowORcol == "row") {
x1 <- GEMatrix[idxvec[1], ]
y1 <- GEMatrix[idxvec[2], ]
}
else if (rowORcol == "col") {
x1 <- GEMatrix[, idxvec[1]]
y1 <- GEMatrix[, idxvec[2]]
}
else {
stop("Error: rowORcol must be \"row\" or \"col\"")
}
getcor <- function(g1, g2, cormethod) {
if (cormethod == "PCC") {
return(cor.test(g1, g2, method = "pearson")$estimate)
}
else if (cormethod == "SCC") {
return(cor.test(g1, g2, method = "spearman")$estimate)
}
else if (cormethod == "KCC") {
return(cor.test(g1, g2, method = "kendall")$estimate)
}
else if (cormethod == "BiWt") {
return(biwt.cor(t(matrix(c(g1, g2), ncol = 2)), output = "vector")[1])
}
else if (cormethod == "GCC") {
return(list(gcc.rankx = onegcc(g1, g2), gcc.ranky = onegcc(g2,
g1)))
}
}
getpvalue <- function(percorvec, pernum, realcor, sigmethod) {
pvalue <- length(which(percorvec >= realcor))/pernum
if (pvalue == 0)
pvalue <- 1/pernum
if (pvalue > 0.5)
pvalue <- 1 - pvalue
if (sigmethod == "two.sided") {
pvalue <- 2 * pvalue
}
return(pvalue)
}
if (length(cormethod) > 1) {
stop("Error: length of cormethod must be of length 1")
}
if (!is.vector(x1) || !is.vector(y1)) {
stop("Error: input two vectors for gcc.corpair")
}
if (!is.numeric(x1) || !is.numeric(y1)) {
stop("Error: x should be numeric")
}
if (length(which(is.na(x1) == TRUE)) > 0 || length(which(is.na(y1) ==
TRUE)) > 0) {
stop("Error: There are Na(s) in x")
}
if (length(x1) != length(y1)) {
stop("Error: the lengths of each row in x are different.\n")
}
realcor <- getcor(x1, y1, cormethod)
if (pernum <= 0) {
if (cormethod == "GCC") {
return(list(gcc.rankx = realcor$gcc.rankx, gcc.ranky = realcor$gcc.ranky,
gcc.rankx.pvalue = NA, gcc.ranky.pvalue = NA))
}
else {
return(list(cor = realcor, pvalue = NA))
}
}
else {
pGCCMatrix <- matrix(0, nrow = pernum, ncol = 2)
colnames(pGCCMatrix) <- c("gcc.rankx", "gcc.ranky")
rownames(pGCCMatrix) <- paste("permut", seq(1, pernum,
by = 1), sep = "")
GenePairXY <- t(matrix(c(x1, y1), ncol = 2))
pGenePairXY <- GenePairXY
Length <- length(x1)
for (i in 1:pernum) {
curtime <- format(Sys.time(), "%H:%M:%OS4")
XXX <- unlist(strsplit(curtime, ":"))
curtimeidx <- (as.numeric(XXX[1]) * 3600 + as.numeric(XXX[2]) *
60 + as.numeric(XXX[3])) * 10000
set.seed(curtimeidx)
TT = sort(runif(Length), index.return = TRUE)$ix
pGenePairXY[1, ] <- GenePairXY[1, TT]
if (cormethod == "GCC") {
cortmp <- getcor(pGenePairXY[1, ], pGenePairXY[2,
], cormethod)
pGCCMatrix[i, 1] <- cortmp$gcc.rankx
pGCCMatrix[i, 2] <- cortmp$gcc.ranky
}
else {
pGCCMatrix[i, 1] <- getcor(pGenePairXY[1, ],
pGenePairXY[2, ], cormethod)
}
}
if (cormethod == "GCC") {
return(list(gcc.rankx = realcor$gcc.rankx, gcc.ranky = realcor$gcc.ranky,
gcc.rankx.pvalue = getpvalue(pGCCMatrix[, 1],
pernum, realcor$gcc.rankx, sigmethod), gcc.ranky.pvalue = getpvalue(pGCCMatrix[,
2], pernum, realcor$gcc.ranky, sigmethod)))
}
else {
return(list(cor = realcor, pvalue = getpvalue(pGCCMatrix[,
1], pernum, realcor, sigmethod)))
}
}
}
<bytecode: 0xdebc3e8>
<environment: namespace:rsgcc>
--- function search by body ---
Function cor.pair in namespace rsgcc has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(GEMatrix) != "matrix") { :
the condition has length > 1
Calls: cor.pair
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.6
Check: examples
Result: ERROR
Running examples in ‘rsgcc-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cor.pair
> ### Title: compute the correlation between two genes
> ### Aliases: cor.pair gcc.cor.pair gcc.corpair
> ### Keywords: correlation
>
> ### ** Examples
>
>
> data(rsgcc) #load the sample data in rsgcc package
> x <- rnaseq[1:4,] #construct a GEMatrix with the RNA-Seq data of the first four genes
>
> #compute correlation between the 1st and 4th genes
> corpair <- cor.pair(c(1,4), GEMatrix = x, rowORcol = "row",
+ cormethod = "GCC", pernum = 0,
+ sigmethod = "two.sided")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
rsgcc
--- call from context ---
cor.pair(c(1, 4), GEMatrix = x, rowORcol = "row", cormethod = "GCC",
pernum = 0, sigmethod = "two.sided")
--- call from argument ---
if (class(GEMatrix) != "matrix") {
stop("Error: GEMatrix should be a numeric data matrix")
}
--- R stacktrace ---
where 1: cor.pair(c(1, 4), GEMatrix = x, rowORcol = "row", cormethod = "GCC",
pernum = 0, sigmethod = "two.sided")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (idxvec, GEMatrix, rowORcol = c("row", "col"), cormethod = c("GCC",
"PCC", "SCC", "KCC", "BiWt"), pernum = 0, sigmethod = c("two.sided",
"one.sided"))
{
onegcc <- function(x, y) {
getrank <- function(datamatrix) {
if (dim(datamatrix)[1] != 2) {
stop("Error: the row num of datamatrix must be 2")
}
OrderIndex <- order(datamatrix[1, ], decreasing = FALSE)
SortGenePair <- datamatrix[, OrderIndex]
Sort2By1 <- SortGenePair[2, ]
return(list(Sort2By1 = Sort2By1, Sort2By2 = sort(datamatrix[2,
], decreasing = FALSE)))
}
gcc <- function(weightvec, vectsort, vectselfsort) {
Sum1 <- sum(weightvec * vectsort)
Sum2 <- sum(weightvec * vectselfsort)
if (Sum2 == 0) {
cat("\n", x, "\n", y, "\n")
cat("Warning: the Denominator is ZRRO, the value of one variable is consistent.")
gcccor <- 0
}
else {
gcccor <- Sum1/Sum2
}
return(gcccor)
}
Length <- length(x)
Wt <- t(2 * seq(1, Length, by = 1) - Length - 1)
GenePairXY <- t(matrix(c(x, y), ncol = 2))
SortYlist <- getrank(GenePairXY)
gcc.rankx <- gcc(Wt, SortYlist$Sort2By1, SortYlist$Sort2By2)
return(gcc.rankx)
}
if (!is.vector(idxvec) | length(idxvec) != 2) {
stop("Error: idxvec must be a vector with two elements indicating the indexs(rows) in GEMatrix")
}
if (class(GEMatrix) != "matrix") {
stop("Error: GEMatrix should be a numeric data matrix")
}
if (rowORcol == "row") {
x1 <- GEMatrix[idxvec[1], ]
y1 <- GEMatrix[idxvec[2], ]
}
else if (rowORcol == "col") {
x1 <- GEMatrix[, idxvec[1]]
y1 <- GEMatrix[, idxvec[2]]
}
else {
stop("Error: rowORcol must be \"row\" or \"col\"")
}
getcor <- function(g1, g2, cormethod) {
if (cormethod == "PCC") {
return(cor.test(g1, g2, method = "pearson")$estimate)
}
else if (cormethod == "SCC") {
return(cor.test(g1, g2, method = "spearman")$estimate)
}
else if (cormethod == "KCC") {
return(cor.test(g1, g2, method = "kendall")$estimate)
}
else if (cormethod == "BiWt") {
return(biwt.cor(t(matrix(c(g1, g2), ncol = 2)), output = "vector")[1])
}
else if (cormethod == "GCC") {
return(list(gcc.rankx = onegcc(g1, g2), gcc.ranky = onegcc(g2,
g1)))
}
}
getpvalue <- function(percorvec, pernum, realcor, sigmethod) {
pvalue <- length(which(percorvec >= realcor))/pernum
if (pvalue == 0)
pvalue <- 1/pernum
if (pvalue > 0.5)
pvalue <- 1 - pvalue
if (sigmethod == "two.sided") {
pvalue <- 2 * pvalue
}
return(pvalue)
}
if (length(cormethod) > 1) {
stop("Error: length of cormethod must be of length 1")
}
if (!is.vector(x1) || !is.vector(y1)) {
stop("Error: input two vectors for gcc.corpair")
}
if (!is.numeric(x1) || !is.numeric(y1)) {
stop("Error: x should be numeric")
}
if (length(which(is.na(x1) == TRUE)) > 0 || length(which(is.na(y1) ==
TRUE)) > 0) {
stop("Error: There are Na(s) in x")
}
if (length(x1) != length(y1)) {
stop("Error: the lengths of each row in x are different.\n")
}
realcor <- getcor(x1, y1, cormethod)
if (pernum <= 0) {
if (cormethod == "GCC") {
return(list(gcc.rankx = realcor$gcc.rankx, gcc.ranky = realcor$gcc.ranky,
gcc.rankx.pvalue = NA, gcc.ranky.pvalue = NA))
}
else {
return(list(cor = realcor, pvalue = NA))
}
}
else {
pGCCMatrix <- matrix(0, nrow = pernum, ncol = 2)
colnames(pGCCMatrix) <- c("gcc.rankx", "gcc.ranky")
rownames(pGCCMatrix) <- paste("permut", seq(1, pernum,
by = 1), sep = "")
GenePairXY <- t(matrix(c(x1, y1), ncol = 2))
pGenePairXY <- GenePairXY
Length <- length(x1)
for (i in 1:pernum) {
curtime <- format(Sys.time(), "%H:%M:%OS4")
XXX <- unlist(strsplit(curtime, ":"))
curtimeidx <- (as.numeric(XXX[1]) * 3600 + as.numeric(XXX[2]) *
60 + as.numeric(XXX[3])) * 10000
set.seed(curtimeidx)
TT = sort(runif(Length), index.return = TRUE)$ix
pGenePairXY[1, ] <- GenePairXY[1, TT]
if (cormethod == "GCC") {
cortmp <- getcor(pGenePairXY[1, ], pGenePairXY[2,
], cormethod)
pGCCMatrix[i, 1] <- cortmp$gcc.rankx
pGCCMatrix[i, 2] <- cortmp$gcc.ranky
}
else {
pGCCMatrix[i, 1] <- getcor(pGenePairXY[1, ],
pGenePairXY[2, ], cormethod)
}
}
if (cormethod == "GCC") {
return(list(gcc.rankx = realcor$gcc.rankx, gcc.ranky = realcor$gcc.ranky,
gcc.rankx.pvalue = getpvalue(pGCCMatrix[, 1],
pernum, realcor$gcc.rankx, sigmethod), gcc.ranky.pvalue = getpvalue(pGCCMatrix[,
2], pernum, realcor$gcc.ranky, sigmethod)))
}
else {
return(list(cor = realcor, pvalue = getpvalue(pGCCMatrix[,
1], pernum, realcor, sigmethod)))
}
}
}
<bytecode: 0x5610c5b7a0b8>
<environment: namespace:rsgcc>
--- function search by body ---
Function cor.pair in namespace rsgcc has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(GEMatrix) != "matrix") { :
the condition has length > 1
Calls: cor.pair
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.6
Check: compiled code
Result: NOTE
File ‘rsgcc/libs/rsgcc.so’:
Found ‘rand_r’, possibly from ‘rand_r’ (C)
Object: ‘points.o’
File ‘rsgcc/libs/rsgcc.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
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: 1.0.6
Check: examples
Result: ERROR
Running examples in ‘rsgcc-Ex.R’ failed
The error most likely occurred in:
> ### Name: cor.pair
> ### Title: compute the correlation between two genes
> ### Aliases: cor.pair gcc.cor.pair gcc.corpair
> ### Keywords: correlation
>
> ### ** Examples
>
>
> data(rsgcc) #load the sample data in rsgcc package
> x <- rnaseq[1:4,] #construct a GEMatrix with the RNA-Seq data of the first four genes
>
> #compute correlation between the 1st and 4th genes
> corpair <- cor.pair(c(1,4), GEMatrix = x, rowORcol = "row",
+ cormethod = "GCC", pernum = 0,
+ sigmethod = "two.sided")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
rsgcc
--- call from context ---
cor.pair(c(1, 4), GEMatrix = x, rowORcol = "row", cormethod = "GCC",
pernum = 0, sigmethod = "two.sided")
--- call from argument ---
if (class(GEMatrix) != "matrix") {
stop("Error: GEMatrix should be a numeric data matrix")
}
--- R stacktrace ---
where 1: cor.pair(c(1, 4), GEMatrix = x, rowORcol = "row", cormethod = "GCC",
pernum = 0, sigmethod = "two.sided")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (idxvec, GEMatrix, rowORcol = c("row", "col"), cormethod = c("GCC",
"PCC", "SCC", "KCC", "BiWt"), pernum = 0, sigmethod = c("two.sided",
"one.sided"))
{
onegcc <- function(x, y) {
getrank <- function(datamatrix) {
if (dim(datamatrix)[1] != 2) {
stop("Error: the row num of datamatrix must be 2")
}
OrderIndex <- order(datamatrix[1, ], decreasing = FALSE)
SortGenePair <- datamatrix[, OrderIndex]
Sort2By1 <- SortGenePair[2, ]
return(list(Sort2By1 = Sort2By1, Sort2By2 = sort(datamatrix[2,
], decreasing = FALSE)))
}
gcc <- function(weightvec, vectsort, vectselfsort) {
Sum1 <- sum(weightvec * vectsort)
Sum2 <- sum(weightvec * vectselfsort)
if (Sum2 == 0) {
cat("\n", x, "\n", y, "\n")
cat("Warning: the Denominator is ZRRO, the value of one variable is consistent.")
gcccor <- 0
}
else {
gcccor <- Sum1/Sum2
}
return(gcccor)
}
Length <- length(x)
Wt <- t(2 * seq(1, Length, by = 1) - Length - 1)
GenePairXY <- t(matrix(c(x, y), ncol = 2))
SortYlist <- getrank(GenePairXY)
gcc.rankx <- gcc(Wt, SortYlist$Sort2By1, SortYlist$Sort2By2)
return(gcc.rankx)
}
if (!is.vector(idxvec) | length(idxvec) != 2) {
stop("Error: idxvec must be a vector with two elements indicating the indexs(rows) in GEMatrix")
}
if (class(GEMatrix) != "matrix") {
stop("Error: GEMatrix should be a numeric data matrix")
}
if (rowORcol == "row") {
x1 <- GEMatrix[idxvec[1], ]
y1 <- GEMatrix[idxvec[2], ]
}
else if (rowORcol == "col") {
x1 <- GEMatrix[, idxvec[1]]
y1 <- GEMatrix[, idxvec[2]]
}
else {
stop("Error: rowORcol must be \"row\" or \"col\"")
}
getcor <- function(g1, g2, cormethod) {
if (cormethod == "PCC") {
return(cor.test(g1, g2, method = "pearson")$estimate)
}
else if (cormethod == "SCC") {
return(cor.test(g1, g2, method = "spearman")$estimate)
}
else if (cormethod == "KCC") {
return(cor.test(g1, g2, method = "kendall")$estimate)
}
else if (cormethod == "BiWt") {
return(biwt.cor(t(matrix(c(g1, g2), ncol = 2)), output = "vector")[1])
}
else if (cormethod == "GCC") {
return(list(gcc.rankx = onegcc(g1, g2), gcc.ranky = onegcc(g2,
g1)))
}
}
getpvalue <- function(percorvec, pernum, realcor, sigmethod) {
pvalue <- length(which(percorvec >= realcor))/pernum
if (pvalue == 0)
pvalue <- 1/pernum
if (pvalue > 0.5)
pvalue <- 1 - pvalue
if (sigmethod == "two.sided") {
pvalue <- 2 * pvalue
}
return(pvalue)
}
if (length(cormethod) > 1) {
stop("Error: length of cormethod must be of length 1")
}
if (!is.vector(x1) || !is.vector(y1)) {
stop("Error: input two vectors for gcc.corpair")
}
if (!is.numeric(x1) || !is.numeric(y1)) {
stop("Error: x should be numeric")
}
if (length(which(is.na(x1) == TRUE)) > 0 || length(which(is.na(y1) ==
TRUE)) > 0) {
stop("Error: There are Na(s) in x")
}
if (length(x1) != length(y1)) {
stop("Error: the lengths of each row in x are different.\n")
}
realcor <- getcor(x1, y1, cormethod)
if (pernum <= 0) {
if (cormethod == "GCC") {
return(list(gcc.rankx = realcor$gcc.rankx, gcc.ranky = realcor$gcc.ranky,
gcc.rankx.pvalue = NA, gcc.ranky.pvalue = NA))
}
else {
return(list(cor = realcor, pvalue = NA))
}
}
else {
pGCCMatrix <- matrix(0, nrow = pernum, ncol = 2)
colnames(pGCCMatrix) <- c("gcc.rankx", "gcc.ranky")
rownames(pGCCMatrix) <- paste("permut", seq(1, pernum,
by = 1), sep = "")
GenePairXY <- t(matrix(c(x1, y1), ncol = 2))
pGenePairXY <- GenePairXY
Length <- length(x1)
for (i in 1:pernum) {
curtime <- format(Sys.time(), "%H:%M:%OS4")
XXX <- unlist(strsplit(curtime, ":"))
curtimeidx <- (as.numeric(XXX[1]) * 3600 + as.numeric(XXX[2]) *
60 + as.numeric(XXX[3])) * 10000
set.seed(curtimeidx)
TT = sort(runif(Length), index.return = TRUE)$ix
pGenePairXY[1, ] <- GenePairXY[1, TT]
if (cormethod == "GCC") {
cortmp <- getcor(pGenePairXY[1, ], pGenePairXY[2,
], cormethod)
pGCCMatrix[i, 1] <- cortmp$gcc.rankx
pGCCMatrix[i, 2] <- cortmp$gcc.ranky
}
else {
pGCCMatrix[i, 1] <- getcor(pGenePairXY[1, ],
pGenePairXY[2, ], cormethod)
}
}
if (cormethod == "GCC") {
return(list(gcc.rankx = realcor$gcc.rankx, gcc.ranky = realcor$gcc.ranky,
gcc.rankx.pvalue = getpvalue(pGCCMatrix[, 1],
pernum, realcor$gcc.rankx, sigmethod), gcc.ranky.pvalue = getpvalue(pGCCMatrix[,
2], pernum, realcor$gcc.ranky, sigmethod)))
}
else {
return(list(cor = realcor, pvalue = getpvalue(pGCCMatrix[,
1], pernum, realcor, sigmethod)))
}
}
}
<bytecode: 0xc486d18>
<environment: namespace:rsgcc>
--- function search by body ---
Function cor.pair in namespace rsgcc has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(GEMatrix) != "matrix") { :
the condition has length > 1
Calls: cor.pair
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.6
Check: examples
Result: ERROR
Running examples in ‘rsgcc-Ex.R’ failed
The error most likely occurred in:
> ### Name: cor.pair
> ### Title: compute the correlation between two genes
> ### Aliases: cor.pair gcc.cor.pair gcc.corpair
> ### Keywords: correlation
>
> ### ** Examples
>
>
> data(rsgcc) #load the sample data in rsgcc package
> x <- rnaseq[1:4,] #construct a GEMatrix with the RNA-Seq data of the first four genes
>
> #compute correlation between the 1st and 4th genes
> corpair <- cor.pair(c(1,4), GEMatrix = x, rowORcol = "row",
+ cormethod = "GCC", pernum = 0,
+ sigmethod = "two.sided")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
rsgcc
--- call from context ---
cor.pair(c(1, 4), GEMatrix = x, rowORcol = "row", cormethod = "GCC",
pernum = 0, sigmethod = "two.sided")
--- call from argument ---
if (class(GEMatrix) != "matrix") {
stop("Error: GEMatrix should be a numeric data matrix")
}
--- R stacktrace ---
where 1: cor.pair(c(1, 4), GEMatrix = x, rowORcol = "row", cormethod = "GCC",
pernum = 0, sigmethod = "two.sided")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (idxvec, GEMatrix, rowORcol = c("row", "col"), cormethod = c("GCC",
"PCC", "SCC", "KCC", "BiWt"), pernum = 0, sigmethod = c("two.sided",
"one.sided"))
{
onegcc <- function(x, y) {
getrank <- function(datamatrix) {
if (dim(datamatrix)[1] != 2) {
stop("Error: the row num of datamatrix must be 2")
}
OrderIndex <- order(datamatrix[1, ], decreasing = FALSE)
SortGenePair <- datamatrix[, OrderIndex]
Sort2By1 <- SortGenePair[2, ]
return(list(Sort2By1 = Sort2By1, Sort2By2 = sort(datamatrix[2,
], decreasing = FALSE)))
}
gcc <- function(weightvec, vectsort, vectselfsort) {
Sum1 <- sum(weightvec * vectsort)
Sum2 <- sum(weightvec * vectselfsort)
if (Sum2 == 0) {
cat("\n", x, "\n", y, "\n")
cat("Warning: the Denominator is ZRRO, the value of one variable is consistent.")
gcccor <- 0
}
else {
gcccor <- Sum1/Sum2
}
return(gcccor)
}
Length <- length(x)
Wt <- t(2 * seq(1, Length, by = 1) - Length - 1)
GenePairXY <- t(matrix(c(x, y), ncol = 2))
SortYlist <- getrank(GenePairXY)
gcc.rankx <- gcc(Wt, SortYlist$Sort2By1, SortYlist$Sort2By2)
return(gcc.rankx)
}
if (!is.vector(idxvec) | length(idxvec) != 2) {
stop("Error: idxvec must be a vector with two elements indicating the indexs(rows) in GEMatrix")
}
if (class(GEMatrix) != "matrix") {
stop("Error: GEMatrix should be a numeric data matrix")
}
if (rowORcol == "row") {
x1 <- GEMatrix[idxvec[1], ]
y1 <- GEMatrix[idxvec[2], ]
}
else if (rowORcol == "col") {
x1 <- GEMatrix[, idxvec[1]]
y1 <- GEMatrix[, idxvec[2]]
}
else {
stop("Error: rowORcol must be \"row\" or \"col\"")
}
getcor <- function(g1, g2, cormethod) {
if (cormethod == "PCC") {
return(cor.test(g1, g2, method = "pearson")$estimate)
}
else if (cormethod == "SCC") {
return(cor.test(g1, g2, method = "spearman")$estimate)
}
else if (cormethod == "KCC") {
return(cor.test(g1, g2, method = "kendall")$estimate)
}
else if (cormethod == "BiWt") {
return(biwt.cor(t(matrix(c(g1, g2), ncol = 2)), output = "vector")[1])
}
else if (cormethod == "GCC") {
return(list(gcc.rankx = onegcc(g1, g2), gcc.ranky = onegcc(g2,
g1)))
}
}
getpvalue <- function(percorvec, pernum, realcor, sigmethod) {
pvalue <- length(which(percorvec >= realcor))/pernum
if (pvalue == 0)
pvalue <- 1/pernum
if (pvalue > 0.5)
pvalue <- 1 - pvalue
if (sigmethod == "two.sided") {
pvalue <- 2 * pvalue
}
return(pvalue)
}
if (length(cormethod) > 1) {
stop("Error: length of cormethod must be of length 1")
}
if (!is.vector(x1) || !is.vector(y1)) {
stop("Error: input two vectors for gcc.corpair")
}
if (!is.numeric(x1) || !is.numeric(y1)) {
stop("Error: x should be numeric")
}
if (length(which(is.na(x1) == TRUE)) > 0 || length(which(is.na(y1) ==
TRUE)) > 0) {
stop("Error: There are Na(s) in x")
}
if (length(x1) != length(y1)) {
stop("Error: the lengths of each row in x are different.\n")
}
realcor <- getcor(x1, y1, cormethod)
if (pernum <= 0) {
if (cormethod == "GCC") {
return(list(gcc.rankx = realcor$gcc.rankx, gcc.ranky = realcor$gcc.ranky,
gcc.rankx.pvalue = NA, gcc.ranky.pvalue = NA))
}
else {
return(list(cor = realcor, pvalue = NA))
}
}
else {
pGCCMatrix <- matrix(0, nrow = pernum, ncol = 2)
colnames(pGCCMatrix) <- c("gcc.rankx", "gcc.ranky")
rownames(pGCCMatrix) <- paste("permut", seq(1, pernum,
by = 1), sep = "")
GenePairXY <- t(matrix(c(x1, y1), ncol = 2))
pGenePairXY <- GenePairXY
Length <- length(x1)
for (i in 1:pernum) {
curtime <- format(Sys.time(), "%H:%M:%OS4")
XXX <- unlist(strsplit(curtime, ":"))
curtimeidx <- (as.numeric(XXX[1]) * 3600 + as.numeric(XXX[2]) *
60 + as.numeric(XXX[3])) * 10000
set.seed(curtimeidx)
TT = sort(runif(Length), index.return = TRUE)$ix
pGenePairXY[1, ] <- GenePairXY[1, TT]
if (cormethod == "GCC") {
cortmp <- getcor(pGenePairXY[1, ], pGenePairXY[2,
], cormethod)
pGCCMatrix[i, 1] <- cortmp$gcc.rankx
pGCCMatrix[i, 2] <- cortmp$gcc.ranky
}
else {
pGCCMatrix[i, 1] <- getcor(pGenePairXY[1, ],
pGenePairXY[2, ], cormethod)
}
}
if (cormethod == "GCC") {
return(list(gcc.rankx = realcor$gcc.rankx, gcc.ranky = realcor$gcc.ranky,
gcc.rankx.pvalue = getpvalue(pGCCMatrix[, 1],
pernum, realcor$gcc.rankx, sigmethod), gcc.ranky.pvalue = getpvalue(pGCCMatrix[,
2], pernum, realcor$gcc.ranky, sigmethod)))
}
else {
return(list(cor = realcor, pvalue = getpvalue(pGCCMatrix[,
1], pernum, realcor, sigmethod)))
}
}
}
<bytecode: 0xd3cff48>
<environment: namespace:rsgcc>
--- function search by body ---
Function cor.pair in namespace rsgcc has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(GEMatrix) != "matrix") { :
the condition has length > 1
Calls: cor.pair
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.6
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘ctc’
Depends: includes the non-default packages:
'biwt', 'cairoDevice', 'fBasics', 'gplots', 'gWidgets',
'gWidgetsRGtk2', 'minerva', 'parmigene', 'stringr', 'snowfall'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Flavor: r-release-osx-x86_64
Version: 1.0.6
Check: compiled code
Result: NOTE
File ‘rsgcc/libs/rsgcc.so’:
Found ‘_rand_r’, possibly from ‘rand_r’ (C)
Object: ‘points.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 1.0.6
Check: package dependencies
Result: NOTE
Depends: includes the non-default packages:
'biwt' 'cairoDevice' 'fBasics' 'gplots' 'gWidgets' 'gWidgetsRGtk2'
'minerva' 'parmigene' 'stringr' 'snowfall'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Flavor: r-oldrel-windows-ix86+x86_64
Version: 1.0.6
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘ctc’
Depends: includes the non-default packages:
‘biwt’ ‘cairoDevice’ ‘fBasics’ ‘gplots’ ‘gWidgets’ ‘gWidgetsRGtk2’
‘minerva’ ‘parmigene’ ‘stringr’ ‘snowfall’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Flavor: r-oldrel-osx-x86_64