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

[William Dunlap]

It looks like a problem in the Matrix package.  I made the file KE.rda
containing the Matrix objects K and E constructed in calc.diffusion.kernel
by adding a save() call just before where R dies in the original example:

        K = lam$values[1] * I - M
        E = I - matrix(1, ncol = ncol(I), nrow = nrow(I))/ncol(I)
cat("saving K, E, etc. in /tmp/KE.rda\n")
save(K, E, deg, invD, I, W, M, lam, file="/tmp/KE.rda")
cat("    done making the file\n")
        K = E %*% K %*% E

With that file in place I get
> library(Matrix)
> load("KE.rda")
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Matrix_1.2-0

loaded via a namespace (and not attached):
[1] grid_3.2.0      lattice_0.20-31
> str(E)
Formal class 'dsyMatrix' [package "Matrix"] with 5 slots
  ..@ x       : num [1:143376676] 1.00 -8.35e-05 -8.35e-05 -8.35e-05
-8.35e-05 ...
  ..@ Dim     : int [1:2] 11974 11974
  ..@ Dimnames:List of 2
  .. ..$ : NULL
  .. ..$ : NULL
  ..@ uplo    : chr "U"
  ..@ factors : list()
> str(K)
Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  ..@ i       : int [1:487692] 0 69 948 951 1027 1192 1414 1420 1421 1714
...
  ..@ p       : int [1:11975] 0 27 125 147 199 212 221 230 254 274 ...
  ..@ Dim     : int [1:2] 11974 11974
  ..@ Dimnames:List of 2
  .. ..$ : chr [1:11974] "GO:0000002" "GO:0000003" "GO:0000012"
"GO:0000018" ...
  .. ..$ : chr [1:11974] "GO:0000002" "GO:0000003" "GO:0000012"
"GO:0000018" ...
  ..@ x       : num [1:487692] 32.2163 -0.004674 -0.000722 -0.005316
-0.014022 ...
  ..@ factors : list()
> EK <- E %*% K
> EKE <- EK %*% E

 *** caught segfault ***
address 0x7fffa7e1ccf8, cause 'memory not mapped'

Traceback:
 1: EK %*% E
 2: EK %*% E

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Wed, May 6, 2015 at 1:57 AM, Martin Maechler <
maechler at lynne.stat.math.ethz.ch> wrote:

> >>>>> lejeczek  <peljasz at yahoo.co.uk>
> >>>>>     on Wed, 6 May 2015 08:20:46 +0100 writes:
>
>     > On 05/05/15 20:36, Duncan Murdoch wrote:
>     >> 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
>     >>
>     > hi Duncan
>     > I remember that this was a principle of most of programming
>     > languages, only a bug in the code and/or compiler could
>     > cause segfault.
>     > In my case it is a contributed package, specifically GOSim
>     > package, I'm not R programmer and I realise my scripting is
>     > far from good and possibly with errors.
>     > I could send that snippet of the code here if people think
>     > it can be looked into and segfault could be replicated?
>     > I also emailed the author.
>
>     > many thanks
>     > P.
>
> Dear P.,
>
> in the case of segfault from using a contributed package,
> you should typically really only email the package maintainer
> (which may different than the package authors), and not R-help.
> Only if the maintainer does not respond at all (and only if the
> package is open source, typically CRAN) should you ask for help here
> or another public forum.
>
> (I would also think it to be polite to the maintainer who has
>  volunteered her/his code to be used by you if you give him an
>  opportunity to see, comment and fix the problem)
>
> Martin Maechler
> ETH Zurich
>
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.
>

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