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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Roleswitch.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Roleswitch_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Roleswitch.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Roleswitch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Roleswitch' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'pracma', 'reshape', 'plotrix', 'microRNA', 'biomaRt', 'Biostrings',
'Biobase', 'DBI'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Roleswitch' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0u5TLT/R.INSTALL17b873f475d2/Roleswitch/man/roleswitch.Rd:42: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0u5TLT/R.INSTALL17b873f475d2/Roleswitch/man/roleswitch.Rd:42: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0u5TLT/R.INSTALL17b873f475d2/Roleswitch/man/roleswitch.Rd:45: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Roleswitch.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
diagnosticPlot: no visible global function definition for 'par'
diagnosticPlot: no visible global function definition for 'axis'
getSeedMatrix: no visible global function definition for 'data'
getTranscriptIDwithLongest3UTR: no visible global function definition
for 'aggregate'
roleswitch: no visible global function definition for 'aggregate'
Undefined global functions or variables:
aggregate axis data par
Consider adding
importFrom("graphics", "axis", "par")
importFrom("stats", "aggregate")
importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'Roleswitch-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diagnosticPlot
> ### Title: Create diagnostic plot for understanding the Roleswitch model
> ### outputs.
> ### Aliases: diagnosticPlot
> ### Keywords: plot
>
> ### ** Examples
>
> x.o <- matrix(abs(rnorm(10, mean=3)),
+ dimnames=list(c(1:10),"mRNA")) # mRNA expression
>
> z.o <- matrix(abs(rnorm(4, mean=3)),
+ dimnames=list(c(1:4),"miRNA")) # miRNA expression
>
> c <- matrix(rpois(40, lambda=3),nrow=nrow(x.o),
+ dimnames=list(c(1:10),c(1:4))) # seed match matrix
>
> rs.pred <- roleswitch(x.o, z.o, c)
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
Roleswitch
--- call from context ---
roleswitch(x.o, z.o, c)
--- call from argument ---
class(x.o) == "eSet" || class(x.o) == "ExpressionSet"
--- R stacktrace ---
where 1: roleswitch(x.o, z.o, c)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x.o, z.o, c, maxiter = 200, tol = 1e-05, eta.z = 0.001,
expected.total = 1.3, verbose = TRUE, annotation.db, probe2genesymbol = TRUE,
...)
{
if (class(x.o) == "eSet" || class(x.o) == "ExpressionSet") {
genes <- featureNames(x.o)
if (probe2genesymbol) {
if (missing(annotation.db) & is.null(annotation(x.o)))
stop("annotation.db or annotation is needed to map probe to gene id")
if (missing(annotation.db) & !is.null(annotation(x.o)))
annotation.db <- sprintf("%s.db", annotation(x.o))
if (is.null(featureNames(x.o)))
stop("featureNames is missing in the eSet/ExpressionSet to map probe id to gene id")
require(annotation.db, character.only = TRUE) ||
stop(sprintf("%s package must be installed",
annotation.db))
probeID <- genes
con_comm <- paste(as.character(strsplit(annotation.db,
split = ".db")), "dbconn", sep = "_")
usedDB <- eval(as.name(con_comm))
con <- usedDB()
annot.s <- dbReadTable(con, "gene_info")
annot.e <- dbReadTable(con, "genes")
annot <- merge(merge(annot.s, annot.e), dbReadTable(con,
"probes"))
genes <- annot[match(probeID, annot$probe_id), "symbol"]
}
if (ncol(x.o) > 1)
warning("mRNA expression matrix has >1 column. Only first column is used.")
x.o <- exprs(x.o)[, 1, drop = F]
if (any(duplicated(genes))) {
message("Average probe values were taken over the same gene.")
df <- aggregate(data.frame(expr = as.numeric(x.o)),
list(genes = genes), mean)
x.o <- as.matrix(df$expr)
rownames(x.o) <- as.matrix(df$genes)
}
else {
rownames(x.o) <- as.matrix(genes)
}
x.o <- x.o[!is.na(rownames(x.o)), , drop = F]
}
if (ncol(z.o) > 1) {
warning("miRNA expression matrix has >1 column. Only first column is used.")
z.o <- z.o[, 1, drop = F]
}
if (missing(c)) {
c <- getSeedMatrix(convert2genesymbol = TRUE, ...)
}
else {
stopifnot(all(dim(c) == c(nrow(x.o), nrow(z.o))))
stopifnot(all(sort(rownames(c)) == sort(rownames(x.o))))
stopifnot(all(sort(colnames(c)) == sort(rownames(z.o))))
}
stopifnot(!is.null(rownames(x.o)) & !is.null(rownames(z.o)) &
!is.null(dimnames(c)))
if (ncol(x.o) > 1)
warning("mRNA expression matrix has >1 column. Only first column is used.")
x.o <- x.o[, 1, drop = F]
if (any(x.o < 0)) {
message("Negative values detected in mRNA expression are set to 0")
x.o[x.o < 0] <- 0
}
if (any(z.o < 0)) {
message("Negative values detected in miRNA expression are set to 0")
z.o[z.o < 0] <- 0
}
if (any(duplicated(rownames(z.o)))) {
message("Average values were taken over the same miRNA.")
df <- aggregate(data.frame(expr = as.numeric(z.o)), list(mirna = rownames(z.o)),
mean)
z.o <- as.matrix(df$expr)
rownames(z.o) <- as.matrix(df$mirna)
}
x.o0 <- x.o
z.o0 <- z.o
genes <- rownames(x.o)
mirna <- rownames(z.o)
c0 <- c[match(rownames(x.o), rownames(c)), match(rownames(z.o),
colnames(c))]
dimnames(c0) <- list(rownames(x.o), rownames(z.o))
c0[is.na(c0)] <- 0
c <- c0
rowidx <- which(apply(c, 1, sum) > 0)
colidx <- which(apply(c, 2, sum) > 0)
c <- c[rowidx, colidx]
x.o <- x.o[rowidx, , drop = F]
z.o <- z.o[colidx, , drop = F]
x.t <- x.o
z.t <- z.o
x.total <- expected.total * sum(x.o)
t <- 1
converged <- FALSE
p.x.prev <- matrix(0, nrow(x.o), nrow(z.o))
p.z.prev <- matrix(0, nrow(x.o), nrow(z.o))
delta.p.all <- 1
if (verbose)
message(sprintf("\nStart roleswitch with %s miRNA and %s mRNA",
nrow(z.o), nrow(x.o)))
while (t < maxiter & !converged) {
t <- t + 1
ex.total <- matrix(rep(t(c) %*% x.t, nrow(x.t)), nrow(x.t),
byrow = T)
ex <- c * matrix(rep(x.t, nrow(z.t)), ncol = nrow(z.t))
rex <- ex.total - ex
p.x <- 1 - exp(matrix(rep(z.t, nrow(x.t)), ncol = nrow(z.t),
byrow = T) * (log(rex) - log(ex.total)))
p.x[is.infinite(p.x) | is.nan(p.x)] <- 0
x.d <- matrix(rep(x.t, nrow(z.t)), ncol = nrow(z.t)) *
p.x * eta.z
x.t <- x.o + apply(x.d, 1, sum)
x.t <- (x.t * x.total)/sum(x.t)
ez.total <- matrix(rep(c %*% z.t, nrow(z.t)), ncol = nrow(z.t))
ez <- c * matrix(rep(t(z.t), nrow(x.t)), nrow = nrow(x.t),
byrow = T)
rez <- ez.total - ez
p.z <- 1 - exp(matrix(rep(x.t, nrow(z.t)), ncol = nrow(z.t)) *
(log(rez) - log(ez.total)))
p.z[is.infinite(p.z) | is.nan(p.z)] <- 0
if (verbose & t > 1)
message(sprintf("%d: max(p.x-p.x.prev)=%.5f", t -
1, max(abs(p.x - p.x.prev))))
delta.p <- max(abs(p.x - p.x.prev))
delta.p2 <- max(abs(p.z - p.z.prev))
delta.p.all <- c(delta.p.all, delta.p)
if (delta.p < tol & delta.p2 < tol) {
converged <- T
}
else {
p.x.prev <- p.x
p.z.prev <- p.z
}
}
if (!identical(rownames(p.x), genes) || !identical(colnames(p.x),
mirna)) {
if (verbose)
message("Some genes or miRNA are left out in calculation\nb/c they have zero target sites or targets!\nTheir probabilities are set to zero in the output matrices")
p.x <- p.x[match(genes, rownames(p.x)), match(mirna,
colnames(p.x))]
p.z <- p.z[match(genes, rownames(p.z)), match(mirna,
colnames(p.z))]
p.x[is.na(p.x)] <- 0
p.z[is.na(p.z)] <- 0
dimnames(p.x) <- dimnames(c0)
dimnames(p.z) <- dimnames(c0)
x.t <- x.t[match(genes, rownames(x.t)), , drop = F]
x.t[is.na(x.t)] <- x.o[is.na(x.t)]
rownames(x.t) <- genes
}
p.xz <- p.x * p.z
promise <- list(x.t = x.t, z.t = z.o0, p.x = p.x, p.z = p.z,
p.xz = p.xz, c = c0, x.o = x.o0, z.o = z.o0, delta.p.all = delta.p.all[-1])
class(promise) <- "ProMISe"
promise
}
<bytecode: 0x0c5b3da0>
<environment: namespace:Roleswitch>
--- function search by body ---
Function roleswitch in namespace Roleswitch has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: length > 1 in coercion to logical
** running examples for arch 'x64' ... ERROR
Running examples in 'Roleswitch-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diagnosticPlot
> ### Title: Create diagnostic plot for understanding the Roleswitch model
> ### outputs.
> ### Aliases: diagnosticPlot
> ### Keywords: plot
>
> ### ** Examples
>
> x.o <- matrix(abs(rnorm(10, mean=3)),
+ dimnames=list(c(1:10),"mRNA")) # mRNA expression
>
> z.o <- matrix(abs(rnorm(4, mean=3)),
+ dimnames=list(c(1:4),"miRNA")) # miRNA expression
>
> c <- matrix(rpois(40, lambda=3),nrow=nrow(x.o),
+ dimnames=list(c(1:10),c(1:4))) # seed match matrix
>
> rs.pred <- roleswitch(x.o, z.o, c)
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
Roleswitch
--- call from context ---
roleswitch(x.o, z.o, c)
--- call from argument ---
class(x.o) == "eSet" || class(x.o) == "ExpressionSet"
--- R stacktrace ---
where 1: roleswitch(x.o, z.o, c)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x.o, z.o, c, maxiter = 200, tol = 1e-05, eta.z = 0.001,
expected.total = 1.3, verbose = TRUE, annotation.db, probe2genesymbol = TRUE,
...)
{
if (class(x.o) == "eSet" || class(x.o) == "ExpressionSet") {
genes <- featureNames(x.o)
if (probe2genesymbol) {
if (missing(annotation.db) & is.null(annotation(x.o)))
stop("annotation.db or annotation is needed to map probe to gene id")
if (missing(annotation.db) & !is.null(annotation(x.o)))
annotation.db <- sprintf("%s.db", annotation(x.o))
if (is.null(featureNames(x.o)))
stop("featureNames is missing in the eSet/ExpressionSet to map probe id to gene id")
require(annotation.db, character.only = TRUE) ||
stop(sprintf("%s package must be installed",
annotation.db))
probeID <- genes
con_comm <- paste(as.character(strsplit(annotation.db,
split = ".db")), "dbconn", sep = "_")
usedDB <- eval(as.name(con_comm))
con <- usedDB()
annot.s <- dbReadTable(con, "gene_info")
annot.e <- dbReadTable(con, "genes")
annot <- merge(merge(annot.s, annot.e), dbReadTable(con,
"probes"))
genes <- annot[match(probeID, annot$probe_id), "symbol"]
}
if (ncol(x.o) > 1)
warning("mRNA expression matrix has >1 column. Only first column is used.")
x.o <- exprs(x.o)[, 1, drop = F]
if (any(duplicated(genes))) {
message("Average probe values were taken over the same gene.")
df <- aggregate(data.frame(expr = as.numeric(x.o)),
list(genes = genes), mean)
x.o <- as.matrix(df$expr)
rownames(x.o) <- as.matrix(df$genes)
}
else {
rownames(x.o) <- as.matrix(genes)
}
x.o <- x.o[!is.na(rownames(x.o)), , drop = F]
}
if (ncol(z.o) > 1) {
warning("miRNA expression matrix has >1 column. Only first column is used.")
z.o <- z.o[, 1, drop = F]
}
if (missing(c)) {
c <- getSeedMatrix(convert2genesymbol = TRUE, ...)
}
else {
stopifnot(all(dim(c) == c(nrow(x.o), nrow(z.o))))
stopifnot(all(sort(rownames(c)) == sort(rownames(x.o))))
stopifnot(all(sort(colnames(c)) == sort(rownames(z.o))))
}
stopifnot(!is.null(rownames(x.o)) & !is.null(rownames(z.o)) &
!is.null(dimnames(c)))
if (ncol(x.o) > 1)
warning("mRNA expression matrix has >1 column. Only first column is used.")
x.o <- x.o[, 1, drop = F]
if (any(x.o < 0)) {
message("Negative values detected in mRNA expression are set to 0")
x.o[x.o < 0] <- 0
}
if (any(z.o < 0)) {
message("Negative values detected in miRNA expression are set to 0")
z.o[z.o < 0] <- 0
}
if (any(duplicated(rownames(z.o)))) {
message("Average values were taken over the same miRNA.")
df <- aggregate(data.frame(expr = as.numeric(z.o)), list(mirna = rownames(z.o)),
mean)
z.o <- as.matrix(df$expr)
rownames(z.o) <- as.matrix(df$mirna)
}
x.o0 <- x.o
z.o0 <- z.o
genes <- rownames(x.o)
mirna <- rownames(z.o)
c0 <- c[match(rownames(x.o), rownames(c)), match(rownames(z.o),
colnames(c))]
dimnames(c0) <- list(rownames(x.o), rownames(z.o))
c0[is.na(c0)] <- 0
c <- c0
rowidx <- which(apply(c, 1, sum) > 0)
colidx <- which(apply(c, 2, sum) > 0)
c <- c[rowidx, colidx]
x.o <- x.o[rowidx, , drop = F]
z.o <- z.o[colidx, , drop = F]
x.t <- x.o
z.t <- z.o
x.total <- expected.total * sum(x.o)
t <- 1
converged <- FALSE
p.x.prev <- matrix(0, nrow(x.o), nrow(z.o))
p.z.prev <- matrix(0, nrow(x.o), nrow(z.o))
delta.p.all <- 1
if (verbose)
message(sprintf("\nStart roleswitch with %s miRNA and %s mRNA",
nrow(z.o), nrow(x.o)))
while (t < maxiter & !converged) {
t <- t + 1
ex.total <- matrix(rep(t(c) %*% x.t, nrow(x.t)), nrow(x.t),
byrow = T)
ex <- c * matrix(rep(x.t, nrow(z.t)), ncol = nrow(z.t))
rex <- ex.total - ex
p.x <- 1 - exp(matrix(rep(z.t, nrow(x.t)), ncol = nrow(z.t),
byrow = T) * (log(rex) - log(ex.total)))
p.x[is.infinite(p.x) | is.nan(p.x)] <- 0
x.d <- matrix(rep(x.t, nrow(z.t)), ncol = nrow(z.t)) *
p.x * eta.z
x.t <- x.o + apply(x.d, 1, sum)
x.t <- (x.t * x.total)/sum(x.t)
ez.total <- matrix(rep(c %*% z.t, nrow(z.t)), ncol = nrow(z.t))
ez <- c * matrix(rep(t(z.t), nrow(x.t)), nrow = nrow(x.t),
byrow = T)
rez <- ez.total - ez
p.z <- 1 - exp(matrix(rep(x.t, nrow(z.t)), ncol = nrow(z.t)) *
(log(rez) - log(ez.total)))
p.z[is.infinite(p.z) | is.nan(p.z)] <- 0
if (verbose & t > 1)
message(sprintf("%d: max(p.x-p.x.prev)=%.5f", t -
1, max(abs(p.x - p.x.prev))))
delta.p <- max(abs(p.x - p.x.prev))
delta.p2 <- max(abs(p.z - p.z.prev))
delta.p.all <- c(delta.p.all, delta.p)
if (delta.p < tol & delta.p2 < tol) {
converged <- T
}
else {
p.x.prev <- p.x
p.z.prev <- p.z
}
}
if (!identical(rownames(p.x), genes) || !identical(colnames(p.x),
mirna)) {
if (verbose)
message("Some genes or miRNA are left out in calculation\nb/c they have zero target sites or targets!\nTheir probabilities are set to zero in the output matrices")
p.x <- p.x[match(genes, rownames(p.x)), match(mirna,
colnames(p.x))]
p.z <- p.z[match(genes, rownames(p.z)), match(mirna,
colnames(p.z))]
p.x[is.na(p.x)] <- 0
p.z[is.na(p.z)] <- 0
dimnames(p.x) <- dimnames(c0)
dimnames(p.z) <- dimnames(c0)
x.t <- x.t[match(genes, rownames(x.t)), , drop = F]
x.t[is.na(x.t)] <- x.o[is.na(x.t)]
rownames(x.t) <- genes
}
p.xz <- p.x * p.z
promise <- list(x.t = x.t, z.t = z.o0, p.x = p.x, p.z = p.z,
p.xz = p.xz, c = c0, x.o = x.o0, z.o = z.o0, delta.p.all = delta.p.all[-1])
class(promise) <- "ProMISe"
promise
}
<bytecode: 0x00000000165ac368>
<environment: namespace:Roleswitch>
--- function search by body ---
Function roleswitch in namespace Roleswitch has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: length > 1 in coercion to logical
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/Roleswitch.Rcheck/00check.log'
for details.