Segfault when running example1

[rogerswt]

Hi Rob,

I'm very interested in trying out citrus. I cloned your repo and successfully installed on a Mac OS X running Yosemite. Went through example 1 using RStudio, and it died... Trying to figure out the problem, I re-ran it in a bare R console. The output is below.

Any suggestions on what I might have done wrong?

Thanks! Wade

> source ("runCitrus.R")
Loading required package: Rclusterpp
Loading required package: Rcpp
Loading required package: RcppEigen
Loading required package: pamr
Loading required package: cluster
Loading required package: survival
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
foreach: simple, scalable parallel programming from Revolution Analytics
Use Revolution R for scalability, fault tolerance and more.
http://www.revolutionanalytics.com
Loaded glmnet 2.0-2

Loading required package: samr
Loading required package: impute
Loading required package: matrixStats
matrixStats v0.50.1 (2015-12-14) successfully loaded. See ?matrixStats for help.
Loading required package: ggplot2
Loading required package: flowCore

Attaching package: ‘flowCore’

The following object is masked from ‘package:Matrix’:

    %&%

Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:flowCore’:

    normalize, parent, tree

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Loading required package: parallel
Loading required package: reshape2
Reading Condition  defaultCondition 
    Reading file  Patient01_healthy.fcs 
    Reading file  Patient02_healthy.fcs 
    Reading file  Patient03_healthy.fcs 
    Reading file  Patient04_healthy.fcs 
    Reading file  Patient05_healthy.fcs 
    Reading file  Patient06_healthy.fcs 
    Reading file  Patient07_healthy.fcs 
    Reading file  Patient08_healthy.fcs 
    Reading file  Patient09_healthy.fcs 
    Reading file  Patient10_healthy.fcs 
    Reading file  Patient11_diseased.fcs 
    Reading file  Patient12_diseased.fcs 
    Reading file  Patient13_diseased.fcs 
    Reading file  Patient14_diseased.fcs 
    Reading file  Patient15_diseased.fcs 
    Reading file  Patient16_diseased.fcs 
    Reading file  Patient17_diseased.fcs 
    Reading file  Patient18_diseased.fcs 
    Reading file  Patient19_diseased.fcs 
    Reading file  Patient20_diseased.fcs 
Clustering 20000 events

 *** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: .Call("hclust_from_data", data = x, link = as.integer(method),     dist = as.integer(distance), p = as.numeric(p), DUP = FALSE,     NAOK = FALSE, PACKAGE = "Rclusterpp")
 2: Rclusterpp.hclust(data)
 3: citrus.cluster.hierarchical(data = c(3.86509871482849,

 ... (long bunch of output) ...

2.00038504600525))
 4: do.call(paste0("citrus.cluster.", clusteringType), args = list(data = citrus.combinedFCSSet$data[,     clusteringColumns]))
 5: citrus.cluster(citrus.combinedFCSSet, clusteringColumns, ...)
 6: citrus.clusterAndMapFolds(citrus.combinedFCSSet, clusteringColumns,     labels = labels, nFolds = nFolds)
 7: citrus.full(fileList = fileList, labels = labels, clusteringColumns = clusteringColumns,     dataDirectory = dataDirectory, outputDirectory = outputDirectory,     family = family, modelTypes = modelTypes, nFolds = nFolds,     fileSampleSize = fileSampleSize, featureType = featureType,     minimumClusterSizePercent = minimumClusterSizePercent, transformColumns = transformColumns,     transformCofactor = transformCofactor, scaleColumns = scaleColumns)
 8: eval(expr, envir, enclos)
 9: eval(ei, envir)
10: withVisible(eval(ei, envir))
11: source("runCitrus.R")

[rogerswt]

Sorry - Just read the FAQ and saw that this is a know issue. My bad! W>

[rogerswt]

Sorry - Just read the FAQ and saw that this is a know issue. My bad! W>