GCRMA segmentation fault
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Entering edit mode
kazi • 0
@kazi-8669
Last seen 5.5 years ago
United States

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")

 

gcrma segmentation fault segfault • 628 views
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Entering edit mode

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()

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Entering edit mode
@james-w-macdonald-5106
Last seen 2 days ago
United States

See here Trouble with gcrma, Segfault on background correction

 

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