Question: GCRMA segmentation fault
0
gravatar for kazi
3.7 years ago by
kazi0
United States
kazi0 wrote:

Getting an extremely reproducible segfault in R versions 3.2.4, 3.2.2, 3.1.0 in Bioconductor versions 3.1 and 3.0 on both 64-bit Windows 10 and 64-bit Centos 6.6.

What causes the error:

affinities <- compute.affinities2("PrimeView")
cels_gcrma <- gcrma(cels, affinity.info = affinities, type = "affinities")

All output:

.Done.
Warning messages:
1: replacing previous import by ‘utils::tail’ when loading ‘primeviewcdf’
2: replacing previous import by ‘utils::head’ when loading ‘primeviewcdf’
3: xy2i is deprecated and will be removed in the next BioC release.
Use xy2indices in the affy package instead.
Adjusting for optical effect.....................................................................................................................................................................................Done.
Adjusting for non-specific binding.
 *** caught segfault ***
address 0x611aaa38, cause 'memory not mapped'

Traceback:
 1: runmed(x[O], 21)
 2: bg.parameters.ns(ncs[index.affinities], anc, apm)
 3: bg.adjust.affinities(pms[, i], ncs = mms[, i], apm = pm.affinities,     anc = mm.affinities, index.affinities, k = k, fast = fast)
 4: gcrma.engine(pms = pm(object), mms = mm(object), ncs, pm.affinities = pm(affinity.info),     mm.affinities = mm(affinity.info), anc, type = type, k = k,     stretch = stretch, correction = correction, GSB.adjust = GSB.adjust,     rho = rho, verbose = verbose, fast = fast)
 5: bg.adjust.gcrma(object, affinity.info = affinity.info, affinity.source = affinity.source,     NCprobe = NCprobe, type = type, k = k, stretch = stretch,     correction = correction, GSB.adjust = GSB.adjust, rho = rho,     optical.correct = optical.correct, verbose = verbose, fast = fast)
 6: gcrma(cels, affinity.info = affinities, type = "affinities")

 

ADD COMMENTlink modified 3.7 years ago by James W. MacDonald52k • written 3.7 years ago by kazi0

The appropriate version of Bioconductor for R-3.2.4 is 3.2. Have you tried that? Please do so and if it still fails, edit your question to include the output of sessionInfo(). 

I tried to run your code but you don't show how cels is defined.

You should run the following to see if your packages are up to date (too old or too new):

source("https://bioconductor.org/biocLite.R")
biocValid()

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Dan Tenenbaum8.2k
Answer: GCRMA segmentation fault
0
gravatar for James W. MacDonald
3.7 years ago by
United States
James W. MacDonald52k wrote:

See here Trouble with gcrma, Segfault on background correction

 

ADD COMMENTlink written 3.7 years ago by James W. MacDonald52k
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