[R] does segfault mean (always) a bug?

lejeczek peljasz at yahoo.co.uk
Wed May 6 10:56:35 CEST 2015

On 06/05/15 09:32, Martin Maechler wrote:
>>>>>> Duncan Murdoch <murdoch.duncan at 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:

#setEvidenceLevel(evidences="all", organism="yeast")
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")

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'

  1: E %*% K %*% E
  2: E %*% K %*% E
  3: calc.diffusion.kernel(method = "diffKernelLLE", m = 5, 
normalization.method = "sqrt",     DIR = "/tmp")
aborting ...


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