[Rd] segfault when unloading a shared library

EJ Nikelski nikelski at bic.mni.mcgill.ca
Thu Aug 13 21:27:05 CEST 2009

Hi All,

   I'm still actively researching this problem (reading R-ext manual),
but I hoped that I might be able to get some additional insight from
the list given that I'm fairly new at writing R extension code.

 Problem:  I have some fairly simple code (.Call interface) that makes
a call to another shared library, which, in turn, calls routines in an
HDF5 shared library.  The good news is that everything works (the
expected value is returned from the HDF5 call); the problem is that R
segfaults when I unload the library.

  I initially suspected that the HDF5 function might be corrupting the
stack/heap, however, if it is, it's not obvious to me.  Upon the
successful return from the function, R responds well, and a gc() call
works without event (only when unloading do I see the problem). In
addition, given that the function returns a  single (double) value, I
passed a much larger array in order to see whether the HDF routine
might be writing off the end of the buffer; the pre-initialized buffer
looked OK upon return.  Interestingly, when I comment out the call to
the HDF routine and manually return a double value, the problem
disappears. So, something within that particular HDF function (other
HDF functions work OK) is messing something up, which is only apparent
at unload time.  Any idea where I should be looking?

The abort output and environment details follow (I don't seem to get a
core dump). Please let me know if any other information might be
helpful, and what I might try next.



> detach(package:mniMincIO)
Unloading shared library: mniMincIO. Library unload path is
now dyn.unload("/Users/jnikelski/R_libs/2.9/mniMincIO/libs/i386/mniMincIO.so")
Unloading shared library mniMincIO in R_unload_mniMincIO

 *** caught segfault ***
address 0xcfa5e0, cause 'memory not mapped'

 1: dyn.unload(file)
 2: library.dynam.unload(libName, file.ext = ".so", verbose = TRUE,
 libpath = libpath)
 3: .Last.lib(libpath)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch(expr, error = function(e) {    call <- conditionCall(e)
 if (!is.null(call)) {        if (identical(call[[1L]],
quote(doTryCatch)))             call <- sys.call(-4L)        dcall <-
deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")
 LONG <- 75L        msg <- conditionMessage(e)        sm <-
strsplit(msg, "\n")[[1L]]        if (14L + nchar(dcall, type = "w") +
nchar(sm[1L], type = "w") >             LONG)             prefix <-
paste(prefix, "\n  ", sep = "")    }    else prefix <- "Error : "
msg <- paste(prefix, conditionMessage(e), "\n", sep = "")
.Internal(seterrmessage(msg[1L]))    if (!silent &&
identical(getOption("show.error.messages"),         TRUE)) {
cat(msg, file = stderr())        .Internal(printDeferredWarnings())
}    invisible(structure(msg, class = "try-error"))})
 8: try(.Last.lib(libpath))
 9: detach(package:mniMincIO)

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: 1
aborting ...
Segmentation fault

> sessionInfo()
R version 2.9.1 (2009-06-26)


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


Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University

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