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Old 05-04-2013, 05:11 AM   #1
Location: Milan

Join Date: May 2013
Posts: 40
Unhappy CummeRbund problem in R with segfault

Hello guys, I am new to R an using it in Mac OSx which I started handling 4 months back. I am using cummeRbund to visualize my data outputs of the cuffdiff analysis and get an idea of the DE genes through different plots. I am unable to create the database after I load the library cummeRbund. When am executing the command cufflinks , it runs for a while and then stops with a segfault error and memory not mapped message. I tried to clear all the cache memory as well but still I am unable to fix it. I have to work on some data urgently and am stuck. It would be nice if you could suggest me something. I am not an expert in R so directly dealing with the diff_exp gene outputs of cuffdiff for creating the matrix and plots is being a bit cumbersome for me. Below are the errors am receiving. Please assist me.

And then when I am calling the library of cummeRbund its is called but as I create the database with the output with readCuffLinks() the below error occurs. Please assist.

Creating database ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/cuffData.db Reading Run Info File ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/ Writing runInfo Table Reading Read Group Info ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/ Writing replicates Table Reading ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/genes.fpkm_tracking Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Reading ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/gene_exp.diff

* caught segfault * address 0x51a41311b, cause 'memory not mapped'

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:

It would be appreciable if you can give me some idea and help me out.

vd4mindia is offline   Reply With Quote
Old 05-30-2013, 06:03 PM   #2
Location: Cambridge, MA

Join Date: Feb 2008
Posts: 82

Can you post the first few lines of your gene_exp.diff file? It may be something in there. I'll be happy to take a look...

lgoff is offline   Reply With Quote

bioinformatic analaysis, cummerbund, r programming, segfault

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