[BioC] Recurrent error with Flashclust
Peter Langfelder
peter.langfelder at gmail.com
Thu Feb 3 17:50:01 CET 2011
Hi Marco,
I'm not on the bioconductor list so I suspect my reply there won't be
let through, but please feel free to forward it if there's interest.
I suspect you are running into limitation of 32-bit integers. Your code shows
>> dim(dataIRDam.cont)
> [1] 48803 7
which means the distance structure has length roughly 48803^2/2, which
is above 2^31. At present the Fortran code uses integers (which I
assume are 4-byte long) and indexing such log arrays may be the root
of the problem.
I'll have to look into this issue. Of course, I can modify the fortran
code to use long integers for indexing, but I need to figure out how
to arrange the interaction with R. Please give me a few days or maybe
a week as I am busy with other stuff as well.
Thanks for alerting me to this issue.
Peter
On Thu, Feb 3, 2011 at 5:15 AM, Manca Marco (PATH)
<m.manca at maastrichtuniversity.nl> wrote:
>
>
> Good afternoon Peter, fellow bioconductors
>
> I have a help request for you.
>
> While planning to use WGCNA on a data set produced through Illumina Humanv3 I am experiencing a recurrent failure of the function flashclust. The output, which lets me without any clue is the following:
>
> *** caught segfault ***
> address 0x7f0222e0d848, cause 'memory not mapped'
>
> *** caught segfault ***
> address 0x3e80000074f, cause 'unknown'
>
>
>
> Following I am pasting all the code and output until the point. Also a sessionInfo() output is pasted at the bottom. I am working an up to date installation of Ubuntu 10.04 64bit and I have updated R (and packages) from CRAN repository and Bioconductor packages using:
> source("http://bioconductor.org/biocLite.R")
> update.packages(repos=biocinstallRepos(), ask=FALSE, checkBuilt=TRUE)
>
>
> Thank you in advance for any direction/feedback you will share with me.
>
> All the best, Marco
>
>
> ###@Workstation1:~$ R
>
> R version 2.12.1 (2010-12-16)
> Copyright (C) 2010 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>> getwd();
> [1] "/home/###"
>> workingDir = "/home/###/Documents/working";
>> setwd(workingDir);
>> library(WGCNA);
> Loading required package: impute
> Loading required package: dynamicTreeCut
> Loading required package: flashClust
>
> Attaching package: 'flashClust'
>
> The following object(s) are masked from 'package:stats':
>
> hclust
>
> Loading required package: qvalue
> Loading Tcl/Tk interface ... done
> Loading required package: Hmisc
> Loading required package: survival
> Loading required package: splines
>
> Attaching package: 'Hmisc'
>
> The following object(s) are masked from 'package:survival':
>
> untangle.specials
>
> The following object(s) are masked from 'package:base':
>
> format.pval, round.POSIXt, trunc.POSIXt, units
>
>
> Package WGCNA version 0.99 loaded.
>
>
> Attaching package: 'WGCNA'
>
> The following object(s) are masked from 'package:stats':
>
> cor
>
>> options(stringsAsFactors = FALSE);
>> library(lumi)
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material. To view, type
> 'openVignette()'. To cite Bioconductor, see
> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>
>
> Attaching package: 'Biobase'
>
> The following object(s) are masked from 'package:Hmisc':
>
> combine, contents
>
> KernSmooth 2.23 loaded
> Copyright M. P. Wand 1997-2009
>
>> fileName <- "FinalReport_nobckgrnd_nonorm.csv";
>>
>> library(illuminaHumanv3BeadID.db)
> Loading required package: AnnotationDbi
> Loading required package: org.Hs.eg.db
> Loading required package: DBI
>>
>> IRDam.dirtyImmature <- lumiR(fileName, convertNuID=FALSE, lib="illuminaHumanv3BeadID.db");
> Perform Quality Control assessment of the LumiBatch object ...
>>
>> IRDam.dirty <- lumiExpresso(IRDam.dirtyImmature, QC.evaluation=TRUE);
> Background Correction: bgAdjust
> Variance Stabilizing Transform method: vst
> Normalization method: quantile
>
>
> Background correction ...
> Perform bgAdjust background correction ...
> There is no control probe information in the LumiBatch object!
> No background adjustment will be performed.
> done.
>
> Variance stabilizing ...
> Perform vst transformation ...
> 2011-02-03 13:11:44 , processing array 1
> ###-Removed for the sake of brevity-###
> done.
>
> Normalizing ...
> Perform quantile normalization ...
> done.
>
> Quality control after preprocessing ...
> Perform Quality Control assessment of the LumiBatch object ...
> done.
>> summary(IRDam.dirty);
> ###-Removed for the sake of brevity-###
>
>> summary(IRDam.dirty, 'QC');
> ###-Removed for the sake of brevity-###
>> dataIRDam.dirty <- exprs(IRDam.dirty)
>>
>> dataIRDam.cont = dataIRDam.dirty[, c(10,11,6,13,22,20,19)]
>> is.matrix(dataIRDam.cont)
> [1] TRUE
>> dim(dataIRDam.cont)
> [1] 48803 7
>> ControlTree1 = flashClust(dist(dataIRDam.cont), method = "average");
>
> *** caught segfault ***
> address 0x7f0222e0d848, cause 'memory not mapped'
>
> *** caught segfault ***
> address 0x3e80000074f, cause 'unknown'
>
> Traceback:
> 1: .Fortran("hc", n = as.integer(n), len = as.integer(len), method = as.integer(method), ia = integer(n), ib = integer(n), crit = double(n), membr = as.double(members), nn = integer(n), disnn = double(n), flag = logical(n), diss = as.double(d))
> 2: hclust(d, method, members)
> 3: flashClust(dist(dataIRDam.cont), method = "average")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
> Traceback:
> 1: .Fortran("hc", n = as.integer(n), len = as.integer(len), method = as.integer(method), ia = integer(n), ib = integer(n), crit = double(n), membr = as.double(members), nn = integer(n), disnn = double(n), flag = logical(n), diss = as.double(d))
> 2: hclust(d, method, members)
> 3: flashClust(dist(dataIRDam.cont), method = "average")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection: Selection:
>
>
>
>
>
> My session info is:
>
>
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8
> [7] LC_PAPER=en_US.utf8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] illuminaHumanv3BeadID.db_1.8.0 org.Hs.eg.db_2.4.6
> [3] RSQLite_0.9-4 DBI_0.2-5
> [5] AnnotationDbi_1.12.0 lumi_2.2.1
> [7] Biobase_2.10.0 WGCNA_0.99
> [9] Hmisc_3.8-3 survival_2.36-2
> [11] qvalue_1.24.0 flashClust_1.00-2
> [13] dynamicTreeCut_1.21 impute_1.24.0
>
> loaded via a namespace (and not attached):
> [1] affy_1.28.0 affyio_1.18.0 annotate_1.28.0
> [4] cluster_1.13.2 grid_2.12.1 hdrcde_2.15
> [7] KernSmooth_2.23-4 lattice_0.19-17 MASS_7.3-9
> [10] Matrix_0.999375-46 methylumi_1.6.1 mgcv_1.7-2
> [13] nlme_3.1-97 preprocessCore_1.12.0 tcltk_2.12.1
> [16] tools_2.12.1 xtable_1.5-6
>
>
> --
> Marco Manca, MD
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML)
> Cardiovascular Research Institute (CARIM)
>
> Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
> Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht
>
> E-mail: m.manca at maastrichtuniversity.nl
> Office telephone: +31(0)433874633
> Personal mobile: +31(0)626441205
> Twitter: @markomanka
>
>
> *********************************************************************************************************************
>
> This email and any files transmitted with it are confi...{{dropped:15}}
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