Re: [Rd] Segfault reporting: memory not mapped error
> Blair Christian
> on Sun, 25 Oct 2009 15:42:36 -0400 writes:
> Is this the right place to report segfaults?
> spc$ R CMD BATCH driver.q rOut.txt
> spc$ tail -16 rOut.txt
/Library/Frameworks/R.framework/Resources/bin/BATCH:
> line 60: 5461 Segmentation fault ${R_HOME}/bin/R -f ${in} ${opts}
> ${R_BATCH_OPTIONS} > ${out} 2>&1
> *** caught segfault ***
> address 0x3f095116, cause 'memory not mapped'
> Traceback:
> 1: .Call("La_dgesv", a, b, tol, PACKAGE = "base")
> 2: solve.default(iV0)
> 3: solve(iV0)
> 4: standardGeneric("solve")
> 5: solve(iV0)
> 6: w0.fullCond(curr.sample, x...@internals@values, x...@priors@values)
> 7: gsSampler(down.univ.gs)
> 8: standardGeneric("gsSampler")
> 9: gsSampler(down.univ.gs)
> 10: univDownStatic(o3Jun21, internal.vals, prior.vals, init.vals,
> param.dims)
> aborting ...
>> sessionInfo()
> R version 2.9.2 (2009-08-24)
> i386-apple-darwin8.11.1
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> I also got this error once:
> Error: segfault from C stack overflow
> Any thoughts would be appreciated. I have no personal C code, and it
looks
> like the matrix I pass to solve is too ill conditioned?
Yes, maybe.
But the underlying LAPACK code that is eventually called from
the above .Call(...)
should *never* seg.fault
On the other hand the "C stack overflow" you've seen is a bad
sign (of other C code your R code calls).
> Let me know what
> other info I can use to help figure out the problem. I saw several of
these
> on the R-help but wasn't sure which was the best place to report.
> Thx, Blair
The most important thing is to provide a self-contained
reproducible example (as the footer of every R-help message has:)
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
Only then there's a good chance that the problem can be
addressed at all.
Martin Maechler, ETH Zurich
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Re: [Rd] mysteriously persistent generic definition
Here's a self-contained example of the problem:
> foo <- function(obj) {return(3);}
> setGeneric("foo")
[1] "foo"
> removeGeneric("foo")
[1] TRUE
> foo <- function(x) {return(4);}
> args(foo)
function (x)
NULL
> setGeneric("foo")
[1] "foo"
> args(foo)
function (obj)
NULL
R 2.7.1. I get the same behavior whether or not I use ESS.
The reason this is more than a theoretical problem:
> setMethod("foo", signature(x="numeric"), function(x) {return(x+4);})
Error in match.call(fun, fcall) : unused argument(s) (x = "numeric")
Ross
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Re: [Rd] mysteriously persistent generic definition
R 2.8.1 on Windows behaves as I expected, i.e., the final args(foo)
returns a function of x. The previous example (below) was on Debian
GNU/Linux.
On Wed, 2009-10-28 at 12:14 -0700, Ross Boylan wrote:
> Here's a self-contained example of the problem:
>
> > foo <- function(obj) {return(3);}
> > setGeneric("foo")
> [1] "foo"
> > removeGeneric("foo")
> [1] TRUE
> > foo <- function(x) {return(4);}
> > args(foo)
> function (x)
> NULL
> > setGeneric("foo")
> [1] "foo"
> > args(foo)
> function (obj)
> NULL
>
> R 2.7.1. I get the same behavior whether or not I use ESS.
>
> The reason this is more than a theoretical problem:
>
> > setMethod("foo", signature(x="numeric"), function(x) {return(x+4);})
> Error in match.call(fun, fcall) : unused argument(s) (x = "numeric")
>
> Ross
>
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Re: [Rd] mysteriously persistent generic definition
On 10/28/2009 3:14 PM, Ross Boylan wrote:
Here's a self-contained example of the problem:
foo <- function(obj) {return(3);}
setGeneric("foo")
[1] "foo"
removeGeneric("foo")
[1] TRUE
foo <- function(x) {return(4);}
args(foo)
function (x)
NULL
setGeneric("foo")
[1] "foo"
args(foo)
function (obj)
NULL
R 2.7.1. I get the same behavior whether or not I use ESS.
The reason this is more than a theoretical problem:
setMethod("foo", signature(x="numeric"), function(x) {return(x+4);})
Error in match.call(fun, fcall) : unused argument(s) (x = "numeric")
We just released 2.10.0. It doesn't have this problem, nor does 2.9.2,
or 2.8.1. I think you'll just have to upgrade.
Duncan Murdoch
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[Rd] unable to compile mgcv
Hello -- I am trying to compile R-2.9.2 on IBM Power5 machine with AIX 5.3. I
have posted three previous posts. Over time I have made significant progress
towards getting a successful build. I am now getting the following error:
==
begin installing recommended package mgcv
* Installing *source* package 'mgcv' ...
** libs
gmake[2]: Entering directory `/tmp/RtmpOtsRnd/R.INSTALL2781446b/mgcv/src'
gcc -maix64 -pthread -std=gnu99 -I/usr/local/builddir/include
-I/usr/local/include -O2 -g -mcpu=power5 -c gcv.c -o gcv.o
gcc -maix64 -pthread -std=gnu99 -I/usr/local/builddir/include
-I/usr/local/include -O2 -g -mcpu=power5 -c gdi.c -o gdi.o
gdi.c: In function 'qr_ldet_inv':
gdi.c:294: error: expected identifier or '(' before numeric constant
gdi.c:308: error: lvalue required as unary '&' operand
gdi.c:308: error: lvalue required as unary '&' operand
gdi.c:316: error: 'j' undeclared (first use in this function)
gdi.c:316: error: (Each undeclared identifier is reported only once
gdi.c:316: error: for each function it appears in.)
gdi.c: In function 'get_detS2a':
gdi.c:617: error: expected identifier or '(' before numeric constant
gdi.c:620: error: 'Mf' undeclared (first use in this function)
gdi.c:636: error: 'max_col' undeclared (first use in this function)
.
ERROR: compilation failed for package 'mgcv'
* Removing '/usr/local/builddir/library/mgcv'
gmake[1]: *** [mgcv.ts] Error 1
gmake[1]: Leaving directory `/usr/local/builddir/src/library/Recommended'
gmake: *** [recommended-packages] Error 2
make: The error code from the last command is 2.
Stop.
==
Initially I had mgcv 1.5-5 and I downloaded mgcv 1.5-6 and tried again. I get
the same error.
I would really appreciate any help with this.
Thanks.
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Re: [Rd] unable to compile mgcv
Some more details on my being able to compile R 2.9.2 for AIX 5.3 export OBJECT_MODE=64 export AR="ar -X64" export R_BROWSER=/opt/freeware/bin/firefox export MAKE=/usr/bin/gmake export R_SHELL=/usr/bin/bash #export LIBICONV=/opt/freeware/lib export CC="gcc -maix64 -pthread" export CXX="g++ -maix64 -pthread" export CFLAGS="-O2 -g -mcpu=power5" export F77="gfortran -maix64 -pthread" export FC="gfortran -maix64 -pthread" export FFLAGS="-O2 -g -mcpu=power5" export FCFLAGS="-O2 -g -mcpu=power5" export CPPFLAGS="-I/usr/lpp/X11/include/X11" export LDFLAGS="-L/usr/lib -L/usr/X11R6/lib -L/usr/local/lib -L/opt/freeware/lib -L/opt/freeware/lib64" === ../R-2.9.2/configure --enable-R-shlib --with-iconv=no > config_292.log 2>&1 ; make > make_292.log 2>&1 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] unable to compile mgcv
The first offending line in gdc.c is
294 int *pivot,i,TRUE=1,j;
and TRUE must be #defined in some AIX
include file. Change it to true or
add #undef TRUE prior to its use and it
may compile.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
> -Original Message-
> From: r-devel-boun...@r-project.org
> [mailto:r-devel-boun...@r-project.org] On Behalf Of Chuck White
> Sent: Wednesday, October 28, 2009 12:47 PM
> To: r-devel@r-project.org
> Subject: [Rd] unable to compile mgcv
>
> Hello -- I am trying to compile R-2.9.2 on IBM Power5 machine
> with AIX 5.3. I have posted three previous posts. Over time
> I have made significant progress towards getting a successful
> build. I am now getting the following error:
>
> ==
> begin installing recommended package mgcv
> * Installing *source* package 'mgcv' ...
> ** libs
> gmake[2]: Entering directory
> `/tmp/RtmpOtsRnd/R.INSTALL2781446b/mgcv/src'
> gcc -maix64 -pthread -std=gnu99 -I/usr/local/builddir/include
> -I/usr/local/include -O2 -g -mcpu=power5 -c gcv.c -o gcv.o
> gcc -maix64 -pthread -std=gnu99 -I/usr/local/builddir/include
> -I/usr/local/include -O2 -g -mcpu=power5 -c gdi.c -o gdi.o
> gdi.c: In function 'qr_ldet_inv':
> gdi.c:294: error: expected identifier or '(' before numeric constant
> gdi.c:308: error: lvalue required as unary '&' operand
> gdi.c:308: error: lvalue required as unary '&' operand
> gdi.c:316: error: 'j' undeclared (first use in this function)
> gdi.c:316: error: (Each undeclared identifier is reported only once
> gdi.c:316: error: for each function it appears in.)
> gdi.c: In function 'get_detS2a':
> gdi.c:617: error: expected identifier or '(' before numeric constant
> gdi.c:620: error: 'Mf' undeclared (first use in this function)
> gdi.c:636: error: 'max_col' undeclared (first use in this function)
> .
> ERROR: compilation failed for package 'mgcv'
> * Removing '/usr/local/builddir/library/mgcv'
> gmake[1]: *** [mgcv.ts] Error 1
> gmake[1]: Leaving directory
> `/usr/local/builddir/src/library/Recommended'
> gmake: *** [recommended-packages] Error 2
> make: The error code from the last command is 2.
>
> Stop.
> ==
>
> Initially I had mgcv 1.5-5 and I downloaded mgcv 1.5-6 and
> tried again. I get the same error.
>
> I would really appreciate any help with this.
>
> Thanks.
>
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Re: [Rd] unable to compile mgcv
Thanks for your response. Can you please point me to the make file where I would make this change. Thanks. William Dunlap wrote: > The first offending line in gdc.c is > 294 int *pivot,i,TRUE=1,j; > and TRUE must be #defined in some AIX > include file. Change it to true or > add #undef TRUE prior to its use and it > may compile. > > Bill Dunlap > Spotfire, TIBCO Software > wdunlap tibco.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] unable to compile mgcv
> -Original Message- > From: Chuck White [mailto:chuckwhi...@charter.net] > Sent: Wednesday, October 28, 2009 3:47 PM > To: r-devel@r-project.org; William Dunlap > Subject: RE: [Rd] unable to compile mgcv > > Thanks for your response. Can you please point me to the > make file where I would make this change. Thanks. If you untar src/library/Recommended/mgcv.tgz (sp?) this file will be in mgcv/src. I'm not sure of the best way to take care of it on AIX. It may be possible to #undef TRUE in include/R.h. The AIX system includes define it in many places, the most prominent of which is in types.h. If you cannot generally #undef TRUE in a global R include file then you will have to edit the C or h files in mgcv. > > William Dunlap wrote: > > The first offending line in gdc.c is > > 294 int *pivot,i,TRUE=1,j; > > and TRUE must be #defined in some AIX > > include file. Change it to true or > > add #undef TRUE prior to its use and it > > may compile. > > > > Bill Dunlap > > Spotfire, TIBCO Software > > wdunlap tibco.com > > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
