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CHECK report for flowType on merida1

This page was generated on 2021-05-06 12:35:00 -0400 (Thu, 06 May 2021).

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 637/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowType 2.28.0  (landing page)
Nima Aghaeepour
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/flowType
Branch: RELEASE_3_12
Last Commit: 237181d
Last Changed Date: 2020-10-27 10:42:00 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: flowType
Version: 2.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowType.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowType_2.28.0.tar.gz
StartedAt: 2021-05-06 01:51:22 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:53:40 -0400 (Thu, 06 May 2021)
EllapsedTime: 137.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: flowType.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowType.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowType_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/flowType.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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:
  countsAndMeans.cpp:73:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  countsAndMeans.cpp:86:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  Warning: Package 'flowType' is deprecated and will be removed from Bioconductor
See ‘/Users/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 sizes of PDF files under ‘inst/doc’ ... OK
* 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: 0x7fdde7306a38>
<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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/flowType.Rcheck/00check.log’
for details.


Installation output

flowType.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowType
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘flowType’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c countsAndMeans.cpp -o countsAndMeans.o
In file included from countsAndMeans.cpp:10:
In file included from ./countsAndMeans.h:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
countsAndMeans.cpp:73:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
        for (register int i = 0; i < marker_count; i++)
             ^~~~~~~~~
countsAndMeans.cpp:86:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
        for (register int i = 0; i < data_count; i++)
             ^~~~~~~~~
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c flowType.cpp -o flowType.o
In file included from flowType.cpp:3:
In file included from ./countsAndMeans.h:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c numberGenerator.cpp -o numberGenerator.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o flowType.so countsAndMeans.o flowType.o numberGenerator.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-flowType/00new/flowType/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'flowType' is deprecated and will be removed from Bioconductor
  version 3.13
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'flowType' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (flowType)

Tests output


Example timings

flowType.Rcheck/flowType-Ex.timings

nameusersystemelapsed
DLBCLExample0.0090.0020.011
HIVData0.1160.0050.122
HIVMetaData0.0020.0020.004
Phenotypes0.0020.0010.002
calcNumPops0.0020.0010.002
decodePhenotype-methods0.0010.0000.002
encodePhenotype0.0000.0010.001