On 06/05/15 09:32, Martin Maechler wrote:
Duncan Murdoch <murdoch.dun...@gmail.com>
on Tue, 5 May 2015 15:36:59 -0400 writes:
> On 05/05/2015 2:54 PM, lejeczek wrote:
>> hi eveybody
>>
>> I'm trying something simple (Biocunductor packages), so
>> simple I believe it's example from docs but I get segfault.
>> I don't suppose incorrect scripting can cause segfault, right?
> In R, a segfault always indicates a bug. What's not so clear is whether
> it is a bug in R, a bug in a contributed package, or a bug in some
> underlying system library.
> If you can only trigger the bug when using a Bioconductor package, then
> the first guess is that it is that package, and the maintainer of that
> package is in the best position to track it down further. If you can
> simplify the code to trigger it without using any contributed packages,
> then it could well be a bug in R, and we'd like to see code to reproduce
it.
> Duncan Murdoch
The bug Duncan mentions can also be in the user's R code, outside any package:
If a user does what (s)he should never do, namely directly call
.C(), .Fortran(), .Call() or similar (.Internal(), .External(),..)
it is typically easy to trigger segfaults, and then the bug is
in the user's R code.
Variations of the above involve using the inline package, or
other interfaces to C/C++/... code, libraries, etc: The bug may be in
your code rather than the underlying code which is allowed to
make strong assumptions about how it is called.
Martin Maechler
not in my case, no of the above call mentioned calls is
being used, it really is very simple code (possibly with errors)
I know this is not a place to debug anything but if one
wants to have a look here it is:
library(org.Hs.eg.db)
#library(org.Mm.eg.db)
#library(org.Sc.sgd.db)
library(GOSim)
#library(GO.db)
#setEvidenceLevel(evidences="all", organism="yeast")
#setEvidenceLevel(evidences="all")
setEvidenceLevel(evidences = "all",
organism=org.Hs.egORGANISM, gomap=org.Hs.egGO)
calc.diffusion.kernel(method="diffKernelLapl", m=5,
normalization.method="sqrt", DIR="/__.aLocalStorages/1")
#calc.diffusion.kernel(method="diffKernelLLE", m=5,
normalization.method="sqrt", DIR="/__.aLocalStorages/1")
and:
...
calculating diffusion kernel 'diffKernelLLE' for ontology BP
using evidence codes 'all' (Homo sapiens) ...
Note: method with signature ‘Matrix#matrix’ chosen for
function ‘-’,
target signature ‘ddiMatrix#matrix’.
"ddiMatrix#ANY" would also be valid
*** caught segfault ***
address 0x7ffedd69e348, cause 'memory not mapped'
Traceback:
1: E %*% K %*% E
2: E %*% K %*% E
3: calc.diffusion.kernel(method = "diffKernelLLE", m = 5,
normalization.method = "sqrt", DIR = "/tmp")
aborting ...
regards
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