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 <
maech...@lynne.stat.math.ethz.ch> wrote:
> >>>>> lejeczek <pelj...@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
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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