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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:flowType.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings flowType_2.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/flowType.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowType/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowType’ version ‘2.28.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘flowType’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'flowType' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.12-bioc/meat/flowType.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
* 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 ... NOTE
Namespace in Imports field not imported from: ‘grDevices’
All declared Imports should be used.
Packages in Depends field not imported from:
‘BH’ ‘Rcpp’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
flowType: no visible global function definition for ‘new’
plot,Phenotypes-flowFrame: no visible global function definition for
‘density’
Undefined global functions or variables:
density new
Consider adding
importFrom("methods", "new")
importFrom("stats", "density")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘flowType-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flowType-package
> ### Title: flowType: Phenotyping Flow Cytometry Assays
> ### Aliases: flowType-package
> ### Keywords: clustering classification HIV FlowCytData
>
> ### ** Examples
>
> #Load the library
> library(flowType)
> data(DLBCLExample)
> MarkerNames <- c('Time', 'FSC-A','FSC-H','SSC-A','IgG','CD38','CD19','CD3','CD27','CD20', 'NA', 'NA')
>
> #These markers will be analyzed
> PropMarkers <- 3:5
> MFIMarkers <- PropMarkers
> MarkerNames <- c('FS', 'SS','CD3','CD5','CD19')
>
> #Run flowType
> Res <- flowType(DLBCLExample, PropMarkers, MFIMarkers, 'kmeans', MarkerNames);
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
flowType
--- call from context ---
flowType(DLBCLExample, PropMarkers, MFIMarkers, "kmeans", MarkerNames)
--- call from argument ---
Methods == "Thresholds" && (!is.list(Thresholds))
--- R stacktrace ---
where 1: flowType(DLBCLExample, PropMarkers, MFIMarkers, "kmeans", MarkerNames)
--- value of length: 3 type: logical ---
kmeans kmeans kmeans
FALSE FALSE FALSE
--- function from context ---
function (Frame, PropMarkers = NULL, MFIMarkers = NULL, Methods = "kmeans",
MarkerNames = NULL, MaxMarkersPerPop = NULL, PartitionsPerMarker = 2,
Thresholds = NULL, MemLimit = 4, verbose = FALSE)
{
if (is.null(PropMarkers))
PropMarkers = c(1:length(exprs(Frame)[1, ]))
if (is.null(MFIMarkers))
MFIMarkers = vector()
if (is.null(MaxMarkersPerPop))
MaxMarkersPerPop <- length(PropMarkers)
if (FALSE %in% is.numeric(PropMarkers))
PropMarkers <- unlist(lapply(1:length(PropMarkers), function(i) {
which(PropMarkers[i] == colnames(exprs(Frame)))
}))
if (FALSE %in% is.numeric(MFIMarkers) && length(MFIMarkers) >
0)
MFIMarkers <- unlist(lapply(1:length(MFIMarkers), function(i) {
which(MFIMarkers[i] == colnames(exprs(Frame)))
}))
VALID_METHODS <- c("Thresholds", "flowMeans", "kmeans", "flowClust")
Methods <- sapply(Methods, function(x) {
sub("thresh", "Thresh", x)
})
if (!all(sapply(Methods, function(x) {
x %in% VALID_METHODS
})))
stop(paste("Invalid method specified. Methods must be one of:",
paste(VALID_METHODS, collapse = ", ")))
if (length(Methods) == 1) {
Methods = rep(Methods, length(PropMarkers))
}
else {
stop("Only one method may be specified")
}
if (Methods == "Thresholds" && (!is.list(Thresholds)))
stop("Thresholds must be provided as a list of vectors.")
if (length(Thresholds) == 1) {
if (length(unique(PartitionsPerMarker)) > 1)
stop("When markers have different numbers of partitions, you must specify Thresholds on a per-marker basis.")
if (length(Thresholds[[1]]) != PartitionsPerMarker[1] -
1)
stop("When a single vector is provided for Thresholds, it must contain exactly PartitionsPerMarker-1 Thresholds.")
Thresholds <- rep(Thresholds, length(PropMarkers))
}
if (length(PartitionsPerMarker) == 1)
PartitionsPerMarker = rep(PartitionsPerMarker, length(PropMarkers))
if (length(PartitionsPerMarker) != length(PropMarkers))
stop("PartitionsPerMarker must either be specified once for all markers, or be of the same length as PropMarkers.")
if (length(Thresholds) == 0 && "Thresholds" %in% Methods)
stop("When Thresholds is specified as a method, You must provide Thresholds via the \"Thresholds\" argument.")
if (is.null(MarkerNames))
MarkerNames <- as.vector(Frame@parameters@data$name)
if (is.null(MarkerNames))
MarkerNames <- PropMarkers
NumPops <- calcNumPops(PartitionsPerMarker, MaxMarkersPerPop)
MemUse <- calcMemUse(NumPops, length(PropMarkers), length(MFIMarkers),
nrow(Frame), MaxMarkersPerPop, max(PartitionsPerMarker))/10^9
if (verbose)
message(sprintf("Estimated memory required: %f GB of RAM",
MemUse))
if (MemUse > MemLimit)
stop(paste("Calling flowType with these parameters would require",
MemUse, "GB of RAM, but MemLimit is", MemLimit, "GB.\n Try reducing MaxMarkersPerPop or the number of MFIMarkers."))
X <- exprs(Frame)[, PropMarkers]
M <- ncol(X)
N <- nrow(X)
Partitions <- matrix(0, M, N)
for (i in 1:M) {
if (Methods[i] == "kmeans") {
km <- kmeans(X[, i], PartitionsPerMarker[i], nstart = 50)$cluster
means <- sapply(unique(km), function(x) {
mean(X[which(km == x), i])
})
names(means) <- unique(km)
means <- sort(means)
new.km <- rep(0, length(km))
for (cluster.ind in 1:PartitionsPerMarker[i]) {
to.replace <- which(names(means) == cluster.ind)
new.km[which(km == cluster.ind)] <- to.replace
}
Partitions[i, ] <- new.km
}
if (Methods[i] == "flowMeans") {
km <- flowMeans(X[, i], NumC = PartitionsPerMarker[i],
MaxN = 10, nstart = 10)@Label
means <- sapply(unique(km), function(x) {
mean(X[which(km == x), i])
})
names(means) <- unique(km)
means <- sort(means)
new.km <- rep(0, length(km))
for (cluster.ind in 1:PartitionsPerMarker[i]) {
to.replace <- which(names(means) == cluster.ind)
new.km[which(km == cluster.ind)] <- to.replace
}
Partitions[i, ] <- new.km
}
if (Methods[i] == "flowClust") {
res <- flowClust(Frame, varNames = colnames(exprs(Frame))[i],
K = PartitionsPerMarker[i], level = 1)
km = map(res@z)
km = replace(km, which(is.na(km)), 1)
means <- sapply(unique(km), function(x) {
mean(X[which(km == x), i])
})
names(means) <- unique(km)
means <- sort(means)
new.km <- rep(0, length(km))
for (cluster.ind in 1:PartitionsPerMarker[i]) {
to.replace <- which(names(means) == cluster.ind)
new.km[which(km == cluster.ind)] <- to.replace
}
Partitions[i, ] <- new.km
}
if (Methods[i] == "Thresholds") {
for (Marker in 1:length(Thresholds)) {
marker.vec <- rep(1, ncol(Partitions))
for (partition in 2:(length(Thresholds[[Marker]]) +
1)) {
marker.vec[which(X[, Marker] >= Thresholds[[Marker]][partition -
1])] <- partition
}
Partitions[Marker, ] <- marker.vec
}
}
}
partToThresh <- function(ThisChan, Partitions, PropMarkers,
ThisExpr) {
if (Methods[ThisChan] == "Thresholds") {
return(Thresholds[[ThisChan]])
}
ThisPart <- t(Partitions)[, ThisChan]
PartLabels <- unique(ThisPart)
MaxParts <- sapply(PartLabels, function(x) {
max(ThisExpr[which(ThisPart == PartLabels[x]), ThisChan])
})
Thresholds <- sort(MaxParts)[1:(length(PartLabels) -
1)]
Thresholds
}
Thresholds <- lapply(1:length(PropMarkers), partToThresh,
Partitions, PropMarkers, X)
for (i in 1:M) {
if (Methods[i] == "flowMeans") {
for (Marker in 1:length(Thresholds)) {
marker.vec <- rep(1, ncol(Partitions))
for (partition in 2:(length(Thresholds[[Marker]]) +
1)) {
marker.vec[which(X[, Marker] >= Thresholds[[Marker]][partition -
1])] <- partition
}
Partitions[Marker, ] <- marker.vec
}
}
}
if (length(MFIMarkers) > 0) {
MFIData <- matrix(exprs(Frame)[, MFIMarkers], ncol = length(MFIMarkers))
}
else {
MFIData <- matrix()
}
res <- .Call("countCells", as.integer(PartitionsPerMarker),
Thresholds, as.integer(MaxMarkersPerPop), PropMarkers,
MFIData, X, NumPops, verbose)
Counts <- res$counts
if (length(MFIMarkers) > 0) {
Means <- res$mfis
Means[which(Counts == 0), ] = NA
}
else {
Means = matrix()
}
Codes <- res$codes
if (length(MFIMarkers) > 0) {
colnames(Means) = colnames(exprs(Frame))[MFIMarkers]
}
Partitions = t(Partitions)
return(new("Phenotypes", CellFreqs = Counts, PhenoCodes = Codes,
MFIs = Means, PropMarkers = PropMarkers, MFIMarkers = MFIMarkers,
MarkerNames = MarkerNames, Partitions = Partitions, PartitionsPerMarker = PartitionsPerMarker,
Thresholds = Thresholds))
}
<bytecode: 0x560c9d5ed750>
<environment: namespace:flowType>
--- function search by body ---
Function flowType in namespace flowType 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: 1 ERROR, 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.12-bioc/meat/flowType.Rcheck/00check.log’
for details.