Hi all,
I have some C++ code that I call from my package. In my main C++ loop, I check
for user interrupts and return to the R shell after ensuring I've deallocated
memory appropriately. This works fine when the code is compiled with gcc+openmp
and with icc without openmp, but when I compile wi
configuration info including native compiler and
operating system versions. Faster response will be obtained by including all
program sources. For information on submitting this issue, please see
http://www.intel.com/software/products/support/.
Thanks,
Ernest
Begin forwarded message:
> From: Ernest Tu
Dear all,
I have wrapped a C++ function in an R package. I allocate/deallocate
memory using C++ 'new' and 'delete'. In order to allow user
interrupts without memory leaks I've moved all the delete statements
required after an interrupt to a separate C++ function freeMemory(),
which is call
On 25 Feb 2007, at 22:21, Ross Boylan wrote:
> On Sun, Feb 25, 2007 at 05:37:24PM +0000, Ernest Turro wrote:
>> Dear all,
>>
>> I have wrapped a C++ function in an R package. I allocate/deallocate
>> memory using C++ 'new' and 'delete'. In order t
On 26 Feb 2007, at 10:51, Hin-Tak Leung wrote:
> Ernest Turro wrote:
>> Dear all,
>> I have wrapped a C++ function in an R package. I allocate/
>> deallocate memory using C++ 'new' and 'delete'. In order to allow
>> user interrupts
Thanks for your comments Ross. A couple more comments/queries below:
On 26 Feb 2007, at 06:43, Ross Boylan wrote:
> [details snipped]
>
> The use of the R api can be confined to a wrapper function. But I can
> think of no reason that a change to the alternate approach I outlined
> would solve th
Hi Simon,
On 26 Feb 2007, at 16:58, Simon Urbanek wrote:
> Ernest,
>
> On Feb 25, 2007, at 12:37 PM, Ernest Turro wrote:
>
>> I have wrapped a C++ function in an R package. I allocate/
>> deallocate memory using C++ 'new' and 'delete'. In order to all
Hi Ross,
On 26 Feb 2007, at 22:34, Ross Boylan wrote:
> On Mon, 2007-02-26 at 16:08 +0000, Ernest Turro wrote:
>> Thanks for your comments Ross. A couple more comments/queries below:
>>
>> On 26 Feb 2007, at 06:43, Ross Boylan wrote:
>>
>>> [details snipped]
[snip]
Sorry. Small mistake fixed below:
>
> Leaving aside the HAVE_AQUA and Win32 cases, I would like to write
> a new function:
>
> int R_CheckInterruptsPending(void)
> {
> R_CheckStack();
> return R_interrupts_pending;
> }
>
> and then in my C++ code:
>
if(R_CheckInterruptsPending)
On 27 Feb 2007, at 17:45, Luke Tierney wrote:
> On Tue, 27 Feb 2007, Ernest Turro wrote:
>
>> Hi Ross,
>>
>> On 26 Feb 2007, at 22:34, Ross Boylan wrote:
>>
>>> On Mon, 2007-02-26 at 16:08 +, Ernest Turro wrote:
>>>> Thanks for your comment
Dear all,
I have a code chunk in my Rnw file that, when executed, outputs
carriage return characters ('\r') to inform on the progress (e.g.
"sweep 4 of 1024\r"). But Sweave interprets this as a newline
character, and therefore I get countless pages of output in my
vignette where I only rea
t how about setting
> "results=hide" in the options of your code chunk?
>
> Best wishes
> Wolfgang
>
> --
> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
>
> Ernest Turro wrote:
>&
Hi,
I'm trying to register my native routines using R_registerRoutines
(...). I can compile the code, but the loader cannot resolve the symbol:
undefined symbol:
_Z18R_registerRoutinesP8_DllInfoPK12R_CMethodDefPK15R_CallMethodDefS3_S6
_
$ nm bgx.Rcheck/bgx/libs/bgx.so | grep R_registerRoutin
On 19 Mar 2007, at 21:32, Duncan Murdoch wrote:
> On 3/19/2007 5:23 PM, Ernest Turro wrote:
>> Hi,
>> I'm trying to register my native routines using R_registerRoutines
>> (...). I can compile the code, but the loader cannot resolve the
>
On 20 Mar 2007, at 00:18, Duncan Murdoch wrote:
> On 3/19/2007 7:41 PM, Ernest Turro wrote:
>> On 19 Mar 2007, at 21:32, Duncan Murdoch wrote:
>>> On 3/19/2007 5:23 PM, Ernest Turro wrote:
>>>> Hi,
>>>> I'm trying to register my native routine
On 20 Mar 2007, at 00:50, Duncan Murdoch wrote:
> On 3/19/2007 8:41 PM, Ernest Turro wrote:
>> On 20 Mar 2007, at 00:18, Duncan Murdoch wrote:
>>> On 3/19/2007 7:41 PM, Ernest Turro wrote:
>>>> On 19 Mar 2007, at 21:32, Duncan Murdoch wrote:
>>>>
Here, I want to show the verbose output and print it onto the tex
file using Sweave to give users a good idea of what happens. What I
don't want is countless lines being printed because \r is being
interpreted as \n ...
Thanks,
Ernest
>>>> Ernest Turro wrote:
>>>>>
Why is it that R places CFLAGS after PKG_CFLAGS and not before when
compiling a package (e.g. through R CMD build pkg)? This can be
problematic if, for instance, you want to use -O3, but -O2 is in
R_HOME/etc/Makeconf. If -O2 (in CFLAGS) appears after -O3 (in
PKG_CFLAGS), you are left with w
elpful. Thanks very much Douglas.
Ernest
>
>> >>>> Ernest Turro wrote:
>> >>>>> Dear all,
>> >>>>> I have a code chunk in my Rnw file that, when executed, outputs
>> >>>>> carriage return characters ('
On 20 Mar 2007, at 21:32, Kasper Daniel Hansen wrote:
>
> On Mar 20, 2007, at 7:58 PM, Ernest Turro wrote:
>
>> Why is it that R places CFLAGS after PKG_CFLAGS and not before when
>> compiling a package (e.g. through R CMD build pkg)? This can be
>> problematic if, fo
It seems unlink doesn't work with wildcards in 2.5.0. I've tried
R-2.5.0 under gnu/linux from source and the Mac binary from att
research. Example:
> dir()
[1] "bgx.Rnw" "bgx.pdf" "run.1"
> unlink("run.*",recursive=T)
> dir()
[1] "bgx.Rnw" "bgx.pdf" "run.1"
> unlink("run.1",recursive=T)
>
glob() should
> work. So try
>
> unlink(Sys.glob("run.*"), recursive=TRUE)
>
>
> On Wed, 25 Apr 2007, Ernest Turro wrote:
>
>> It seems unlink doesn't work with wildcards in 2.5.0. I've tried
>> R-2.5.0 under gnu/linux from source and the Mac b
Hi,
R 2.5.0 isn't auto-completing paths properly as it used to. E.g.
suppose I have:
> dir("CEL/choe")
[1] "chipC-rep1.CEL" "chipC-rep2.CEL" "chipC-rep3.CEL" "chipS-rep1.CEL"
[5] "chipS-rep2.CEL" "chipS-rep3.CEL"
Now if I do:
ReadAffy("CEL/choe/ch # => ReadAffy("CEL/choe/chip
ReadAffy("CEL/c
you posted such a comment about something
> highlighted under USER-VISIBLE CHANGES as a configurable option.
>
> R-devel has an option to fine-tune this behaviour.
>
>
> On Thu, 26 Apr 2007, Ernest Turro wrote:
>
>> Hi,
>>
>> R 2.5.0 isn't auto-completing paths pro
tempdir() on windows returns the path using "\\" as file separator.
But .Platform$file.sep returns "/". As a result, you get
inconsistencies like:
> file.path(tempdir(), "foo")
[1] "C:\\WINDOWS\\Temp\\RtmpYEIXrb/foo" # Mix of \\ and /
I'm not sure if this can cause problems but I thought I'
Dear all,
If one specifies, say, "PKG_CXXFLAGS= -O3" in a Makevars file, it
will not make a difference to how the code is compiled if -O2 is
specified in $R_HOME/etc/Makeconf. This is because PKG_CXXFLAGS is
prepended to the corresponding flags in $R_HOME/etc/Makeconf instead
of being appe
Dear all,
R on Macports relies on GCC 4.3 to build packages. I find that
packages with shared objects that use C++ streams crash R if they're
compiled using Macports' gcc43, but work fine if compiled in exactly
the same way using Apple-supplied GCC 4.2. Has anyone here had the
same issue/
On 30 Jul 2008, at 15:46, Simon Urbanek wrote:
On Jul 30, 2008, at 9:45 , Ernest Turro wrote:
Dear all,
R on Macports relies on GCC 4.3 to build packages. I find that
packages with shared objects that use C++ streams crash R if
they're compiled using Macports' gcc43, but wo
he console, there is no indication that doing this may crash R
(and this has never happened to me before). Certainly, the use of file
streams (fstreams) should work just fine.
Ernest
Kjell
On Jul 30, 2008, at 3:45 PM, Ernest Turro wrote:
Dear all,
R on Macports relies on GCC 4.3 to buil
On 30 Jul 2008, at 18:04, Simon Urbanek wrote:
On Jul 30, 2008, at 12:32 , Ernest Turro wrote:
On 30 Jul 2008, at 15:46, Simon Urbanek wrote:
On Jul 30, 2008, at 9:45 , Ernest Turro wrote:
Dear all,
R on Macports relies on GCC 4.3 to build packages. I find that
packages with shared
On 30 Jul 2008, at 17:58, Simon Urbanek wrote:
On Jul 30, 2008, at 12:35 , Ernest Turro wrote:
On 30 Jul 2008, at 15:18, Kjell Konis wrote:
I found this in Writing R Extensions:
"Using C++ iostreams, as in this example, is best avoided. There
is no guarantee that the output
On 30 Jul 2008, at 19:23, Simon Urbanek wrote:
On Jul 30, 2008, at 13:16 , Ernest Turro wrote:
On 30 Jul 2008, at 18:04, Simon Urbanek wrote:
On Jul 30, 2008, at 12:32 , Ernest Turro wrote:
On 30 Jul 2008, at 15:46, Simon Urbanek wrote:
On Jul 30, 2008, at 9:45 , Ernest Turro
On 30 Jul 2008, at 20:25, Simon Urbanek wrote:
On Jul 30, 2008, at 15:13 , Ernest Turro wrote:
On 30 Jul 2008, at 19:23, Simon Urbanek wrote:
On Jul 30, 2008, at 13:16 , Ernest Turro wrote:
On 30 Jul 2008, at 18:04, Simon Urbanek wrote:
On Jul 30, 2008, at 12:32 , Ernest Turro
R --vanilla < foo.R
# Don't crash:
g++-4.2 -shared -fPIC foo.cc -o foo.so
R --vanilla < foo.R
Kjell
On Jul 30, 2008, at 6:32 PM, Ernest Turro wrote:
On 30 Jul 2008, at 15:46, Simon Urbanek wrote:
On Jul 30, 2008, at 9:45 , Ernest Turro wrote:
Dear all,
R on Macports r
How should one go about including data files for use by some C
function in an R package? The data subdirectory is for additional data
files the package makes available for loading from R, not C, and
including the files in some other directory is no good because non-
standard directories are
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