On 4/23/2007 10:56 AM, Sebastian Weber wrote:> Hello everybody,
>
> I'm using hdf5 files to store results from intermediate calculations.
> These are usually part of a list, called "res". As I want the
hdf-files
> to contain all the members of res in its top "directory", I used
to do
>
> attach(res)
> do.call("hdf5save", args=c(fileout=file.path(dir, ofile),
> as.list(names(res))))
> detach(res)
>
> which did what I wanted (R version 2.3.1 under ubuntu edgy). Since the
> upgrade to ubuntu feisty fawn which ships with R 2.4.1, the code above
> causes a crash:
>
> *** caught segfault ***
> address 0x11, cause 'memory not mapped'
>
> Traceback:
> 1: .External("do_hdf5save", call, sys.frame(sys.parent()),
> fileout, ..., PACKAGE = "hdf5")
> 2: hdf5save(fileout >
"tex/ABpattern_pub/data/knnTest/gTest_annAB.1.statsAll.hdf5",
> "newman", "hist", "graphProp",
"graphBins")
> 3: do.call("hdf5save", args = c(fileout = file.path(dir, ofile),
> as.list(names(res))))
> 4: avgGraphData(dir = "tex/ABpattern_pub/data/knnTest")
>
> Any ideas on how to fix this or what is wrong? To me it seems to be a
> bug introduced in R 2.4.1.
hdf5save is a function in the hdf5 contributed package, so you should
start with its maintainer, Marcus G. Daniels <mdaniels at lanl.gov>. But
before you bother him, make sure you're using the latest release of it.
If you still have problems, give him the usual details requested in
the posting guide.
Duncan Murdoch