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 confide...{{dropped:15}}

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}}