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CHECK report for flowType on tokay2

This page was generated on 2020-10-17 11:56:35 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE flowType PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 629/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowType 2.26.0
Nima Aghaeepour
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/flowType
Branch: RELEASE_3_11
Last Commit: 68e908c
Last Changed Date: 2020-04-27 14:26:04 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR  OK 

Summary

Package: flowType
Version: 2.26.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowType.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowType_2.26.0.tar.gz
StartedAt: 2020-10-17 04:09:40 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:12:18 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 157.8 seconds
RetCode: 1
Status:  ERROR  
CheckDir: flowType.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowType.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowType_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/flowType.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 'flowType/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowType' version '2.26.0'
* 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 whether package 'flowType' can be installed ... OK
* 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 ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowType/libs/i386/flowType.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowType/libs/x64/flowType.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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: 0x0e05f798>
<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

** running examples for arch 'x64' ... 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: 0x000000001a63ca68>
<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: 2 ERRORs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/flowType.Rcheck/00check.log'
for details.


Installation output

flowType.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/flowType_2.26.0.tar.gz && rm -rf flowType.buildbin-libdir && mkdir flowType.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowType.buildbin-libdir flowType_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL flowType_2.26.0.zip && rm flowType_2.26.0.tar.gz flowType_2.26.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  843k  100  843k    0     0  11.7M      0 --:--:-- --:--:-- --:--:-- 12.8M

install for i386

* installing *source* package 'flowType' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c countsAndMeans.cpp -o countsAndMeans.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c flowType.cpp -o flowType.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c numberGenerator.cpp -o numberGenerator.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o flowType.dll tmp.def countsAndMeans.o flowType.o numberGenerator.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/flowType.buildbin-libdir/00LOCK-flowType/00new/flowType/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowType'
    finding HTML links ... done
    DLBCLExample                            html  
    HIVData                                 html  
    HIVMetaData                             html  
    Phenotypes                              html  
    calcMemUse                              html  
    calcNumPops                             html  
    decodePhenotype-methods                 html  
    encodePhenotype                         html  
    flowType-package                        html  
    flowType                                html  
    getLabels                               html  
    plot                                    html  
    summary-methods                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'flowType' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c countsAndMeans.cpp -o countsAndMeans.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c flowType.cpp -o flowType.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c numberGenerator.cpp -o numberGenerator.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o flowType.dll tmp.def countsAndMeans.o flowType.o numberGenerator.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/flowType.buildbin-libdir/flowType/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowType' as flowType_2.26.0.zip
* DONE (flowType)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'flowType' successfully unpacked and MD5 sums checked

Tests output


Example timings

flowType.Rcheck/examples_i386/flowType-Ex.timings

nameusersystemelapsed
DLBCLExample0.010.030.05
HIVData0.190.020.20
HIVMetaData000
Phenotypes000
calcNumPops0.010.000.02
decodePhenotype-methods000
encodePhenotype000

flowType.Rcheck/examples_x64/flowType-Ex.timings

nameusersystemelapsed
DLBCLExample0.020.000.02
HIVData0.110.000.11
HIVMetaData000
Phenotypes000
calcNumPops000
decodePhenotype-methods000
encodePhenotype000