Error (segmentation fault) when launching AnnotateDiffreport

January 22, 2014, 02:41:46 AM

Hi everybody,

For some months, we are getting an error (*** caught segfault ***) when we lauch AnnotateDiffreport on our cluster. We have searched many times but we are desperate. Did anybody ever get this bug when launching annotatediffreport?

Thanks in advance

,

Mish

Error we get:

*** caught segfault ***
address (nil), cause 'unknown
Traceback:
1: .Call("BGL_highly_conn_sg", as.integer(nv), as.integer(ne), as.integer(em - 1), as.double(rep(1, ne)), as.integer(sat), as.integer(lldv), as.integer(ldv), PACKAGE = "RBGL")
2: highlyConnSG(g)
3: .local(object, ...)
4: calcPC.hcs(object, ...)
5: calcPC.hcs(object, ...)
6: do.call(method, alist(object, ...))
7: calcPC(object, method = graphMethod, ajc = resMat, psg_list = psg_list)
8: calcPC(object, method = graphMethod, ajc = resMat, psg_list = psg_list)
9: .local(object, cor_eic_th, pval, graphMethod, calcIso, calcCiS, calcCaS, psg_list, xraw, cor_exp_th, ...)
10: groupCorr(xa, cor_eic_th = cor_eic_th, psg_list = psg_list)
11: groupCorr(xa, cor_eic_th = cor_eic_th, psg_list = psg_list)
12: annotateDiffreport(<S4 object of class "xcmsSet">, eicmax = 10, eicwidth = 200, metlin = 0, sortpval = "TRUE", nSlaves = 9, sigma = 6, perfwhm = 0.6, maxcharge = 3, maxiso = 4, minfrac = 0.5, ppm = 5, mzabs = 0.015, quick = "FALSE", cor_eic_th = 0.75, graphMethod = "hcs", pval = 0.05, calcCiS = "TRUE", calcIso = "FALSE", calcCaS = "FALSE", polarity = "negative", multiplier = 3, class1 = "Urines_Controles_A", class2 = "Urines_Controles_B", filebase = "Urines_Controles_A_vs_Urines_Controles_B")
13: do.call(thefunction, listArguments)

Re: Error (segmentation fault) when launching AnnotateDiffre

Reply #1 – January 22, 2014, 10:31:28 PM

This problem has nothing to do with CAMERA, but with highlyConnSG() in the RBGL library.
Can you try updating/reinstalling RBGL ?

Re: Error (segmentation fault) when launching AnnotateDiffre

Reply #2 – February 05, 2015, 07:41:06 AM

Hi,

Thank you very much for your advice, you are right, i updated the RGBL package and it solved my problem.

Thank you again,

Cheers,

Misharl Monsoor.