[BioC] Recurrent error with Flashclust
Manca Marco (PATH)
m.manca at maastrichtuniversity.nl
Thu Feb 3 14:15:38 CET 2011
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
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