Entering edit mode
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")
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
celsis 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()