Re: [Rd] Installation problem from R 2.8.x
True, /tmp is noexec and this is generally a good practice for system security. Okay, I'll define TMPDIR=$HOME/tmp for the R package admin on our systems. I think it'd be good if R developers could consider to add something like: If $TMPDIR is not executable, then EITHER "error message" OR "mkdir $HOME/tmp; chmod u+x $HOME/tmp; TMPDIR=$HOME/tmp; export TMPDIR" in src/library/tools/R/install.R or wherever you seem to fit. Regards, Zong-Pei On Wed, 30 Sep 2009, William Dunlap wrote: Date: Wed, 30 Sep 2009 10:30:32 -0700 From: William Dunlap To: Uwe Ligges , zong-pei@imm.ox.ac.uk Cc: r-devel@r-project.org Subject: RE: [Rd] Installation problem from R 2.8.x In September 2009 Matias Silva reported a execution permission problem during a package installation (look in the r-devel archives for ' [Rd] Installing rJava RJDBC bad interpreter: Permission denied'). It was due to the fstab file marking /tmp as noexec, hence nothing in /tmp was executable, regardless of its file mode. Since the package was copied to /tmp before compilation he ran into the problem. I think he worked around it by setting TMPDIR=/var/tmp, where /var/tmp did not have this restriction, before doing the install. His error message was different but you might be having a similar problem. Bill Dunlap TIBCO Software Inc - Spotfire Division wdunlap tibco.com > -Original Message- > From: r-devel-boun...@r-project.org > [mailto:r-devel-boun...@r-project.org] On Behalf Of Uwe Ligges > Sent: Wednesday, September 30, 2009 9:49 AM > To: zong-pei@imm.ox.ac.uk > Cc: r-devel@r-project.org > Subject: Re: [Rd] Installation problem from R 2.8.x > > What you call a bug in R has never been reported since R-2.8.0 was > recent. Hence I guess it is a permission issue on your system. > Or do you think nobody else tried to install a package during > the last > 12 months? > > Uwe Ligges > > > zong-pei@imm.ox.ac.uk wrote: > > Dear Developers, > > > > Since 2.8, R installation has got a bug in it such > > that if a package has a "configure" file then it > > cannot be installed without modification. > > > > For example: > > > > * Installing *source* package 'foreign' ... > > ERROR: 'configure' exists but is not executable -- > > see the 'R Installation and Adminstration Manual' > > * Removing '/usr/local/source_code/Linux/R/R-2.9.2/library/foreign' > > make[2]: *** [foreign.ts] Error 1 > > > > In fact, 'configure' is executable!!! So I have to manually > > run 'configure', remove 'configure', and then repackage > > foreign_0.8-37.tar.gz so it can be installed. > > > > This bug makes it very time consuming to add any package > > which has a 'configure' in it. And the bug seems to be > > in src/library/tools/R/install.R > > > > Regards, > > > > Dr Zong-Pei Han > > UNIX Systems Administrator > > Computational Biology Research Group > > University of Oxford > > http://www.cbrg.ox.ac.uk/ > > > > __ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Dependency 'sma' is not available
So packages like beadarray and arrayQualityMetrics cannot be installed. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Dependency 'sma' is not available
zong-pei@imm.ox.ac.uk wrote:
> So packages like beadarray and arrayQualityMetrics
> cannot be installed.
The sma author no longer wishes to maintain this package. The packges
beadarray and arrayQualityMetrics are Bioconductor packages that depend
on sma indirectly through other packages. The other packages are being
revised to no longer depend on sma, but this has not yet been completed.
The workaround is to manually install sma from its archive: download
http://cran.fhcrc.org/src/contrib/Archive/sma/sma_0.5.15.tar.gz
and install.packages("sma_0.5.15.tar.gz", repos=NULL).
beadarray and arrayQualityMetrics are Bioconductor packages, so please
follow up on the Bioconductor mailing list
http://bioconductor.org/docs/mailList.html
Martin
>
> __
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[Rd] creating environments in package's C code
Dear developers, is it possible to create environments in C code of packages? Simply using SEXP env; PROTECT (env = allocSExp(ENVSXP)); and assigning the enclosing environment with SET_ENCLOS seems to be insufficient. Best wishes, Martin -- Dr. Martin Becker Statistics and Econometrics Saarland University Campus C3 1, Room 206 66123 Saarbruecken Germany __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] creating environments in package's C code
Martin Becker wrote:
Dear developers,
is it possible to create environments in C code of packages?
Simply using
SEXP env;
PROTECT (env = allocSExp(ENVSXP));
and assigning the enclosing environment with SET_ENCLOS seems to be
insufficient.
Best wishes,
Here's a function I use in rapache to create one:
static SEXP NewEnv(SEXP enclos){
SEXP env;
PROTECT(env = allocSExp(ENVSXP));
SET_FRAME(env, R_NilValue);
SET_ENCLOS(env, (enclos)? enclos: R_GlobalEnv);
SET_HASHTAB(env, R_NilValue);
SET_ATTRIB(env, R_NilValue);
UNPROTECT(1);
return env;
}
and an example that creates a new environment and then assigns a
variable named OK an integer vector length 1 with value 0:
SEXP env = NewEnv(R_GlobalEnv);
defineVar(install("OK"),NewInteger(0),env);
Best
Jeff
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Re: [Rd] creating environments in package's C code
On Oct 1, 2009, at 11:33 , Martin Becker wrote: Dear developers, is it possible to create environments in C code of packages? Simply using SEXP env; PROTECT (env = allocSExp(ENVSXP)); and assigning the enclosing environment with SET_ENCLOS seems to be insufficient. Rf_NewEnvironment is the function that does it, e.g., Rf_NewEnvironment(R_NilValue, R_NilValue, parent) it's not part of the official API (headers) but it is visible. For hashed environments it's R_NewHashedEnv(). Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] creating environments in package's C code
Jeff Horner wrote:
Martin Becker wrote:
Dear developers,
is it possible to create environments in C code of packages?
Simply using
SEXP env;
PROTECT (env = allocSExp(ENVSXP));
and assigning the enclosing environment with SET_ENCLOS seems to be
insufficient.
Best wishes,
Here's a function I use in rapache to create one:
static SEXP NewEnv(SEXP enclos){
SEXP env;
PROTECT(env = allocSExp(ENVSXP));
SET_FRAME(env, R_NilValue);
SET_ENCLOS(env, (enclos)? enclos: R_GlobalEnv);
SET_HASHTAB(env, R_NilValue);
SET_ATTRIB(env, R_NilValue);
UNPROTECT(1);
return env;
}
Oops! I forgot the definition of my simple function NewInteger:
static SEXP NewInteger(int i){
SEXP val;
PROTECT(val = NEW_INTEGER(1));
INTEGER_DATA(val)[0] = i;
UNPROTECT(1);
return val;
}
and an example that creates a new environment and then assigns a
variable named OK an integer vector length 1 with value 0:
SEXP env = NewEnv(R_GlobalEnv);
defineVar(install("OK"),NewInteger(0),env);
Best
Jeff
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[Rd] Rd.sty question: LaTeX expert needed
The Rd.sty LaTeX package is used when building the R manuals, and by the
LaTeX pages produced from the man pages.
I have tracked down some problems Gábor Csárdi was having recently (see
"Re: [R] preformatted and '#' in manual pages" in R-help) to a LaTeX
problem, and am trying to work out how to fix it.
Specifically, the .Rd file he was using had a structure like
\dQuote{
...
\preformatted{
line 1
line 2
}
}
which tools::Rd2latex in R translates to the similar LaTeX code
\dQuote{
...
\begin{alltt}
line 1
line 2
\end{alltt}
}
The problem is that the alltt environment (which is a sort of verbatim
environment, except macros are allowed) doesn't work when embedded like
this in the \dQuote{} macro. Gábor was getting errors when his line 1
contained a # symbol, and when I dealt with that, I found the formatting
was getting messed up, and the section ended up being rendered as
line 1 line 2
The \dQuote macro has a simple definition in Rd.sty as
\newcommand{\dQuote}[1]{``#1''}
so I expect the same error will happen with many other macros in Rd.sty.
So, my questions: Is there a known workaround for this in alltt?
If not, I could skip the macro expansion of \dQuote by generating the
quotes directly in Rd2latex, and most other macros could be handled
similarly. However, then nobody who uses Rd.sty would be able to
redefine the look of those macros and have things display properly.
A third possibility is that we could make it illegal to nest
\preformatted within other macros, but that seems to be an unfortunate
limitation.
Any help would be appreciated.
Duncan Murdoch
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Re: [Rd] creating environments in package's C code
Jeff,
On Oct 1, 2009, at 12:37 , Jeff Horner wrote:
Jeff Horner wrote:
Martin Becker wrote:
Dear developers,
is it possible to create environments in C code of packages?
Simply using
SEXP env;
PROTECT (env = allocSExp(ENVSXP));
and assigning the enclosing environment with SET_ENCLOS seems to
be insufficient.
Best wishes,
Here's a function I use in rapache to create one:
static SEXP NewEnv(SEXP enclos){
SEXP env;
PROTECT(env = allocSExp(ENVSXP));
SET_FRAME(env, R_NilValue);
SET_ENCLOS(env, (enclos)? enclos: R_GlobalEnv);
SET_HASHTAB(env, R_NilValue);
SET_ATTRIB(env, R_NilValue);
UNPROTECT(1);
return env;
}
eek ... that some dangerous bit of code ;). I think Rf_NewEnviroment
is safer even if it's not the headers :P.
Oops! I forgot the definition of my simple function NewInteger:
static SEXP NewInteger(int i){
SEXP val;
PROTECT(val = NEW_INTEGER(1));
INTEGER_DATA(val)[0] = i;
UNPROTECT(1);
return val;
}
I suspect you like reinventing the wheel ;). Your NewInteger is part
of the R API and is called ScalarInteger(). When you need something,
chances are that R has it already, so it's worth greping through the
headers (and sometimes even through the main sources).
Cheers,
Simon
and an example that creates a new environment and then assigns a
variable named OK an integer vector length 1 with value 0:
SEXP env = NewEnv(R_GlobalEnv);
defineVar(install("OK"),NewInteger(0),env);
Best
Jeff
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Re: [Rd] creating environments in package's C code
On 10/1/2009 12:37 PM, Jeff Horner wrote:
Jeff Horner wrote:
Martin Becker wrote:
Dear developers,
is it possible to create environments in C code of packages?
Simply using
SEXP env;
PROTECT (env = allocSExp(ENVSXP));
and assigning the enclosing environment with SET_ENCLOS seems to be
insufficient.
Best wishes,
Here's a function I use in rapache to create one:
static SEXP NewEnv(SEXP enclos){
SEXP env;
PROTECT(env = allocSExp(ENVSXP));
SET_FRAME(env, R_NilValue);
SET_ENCLOS(env, (enclos)? enclos: R_GlobalEnv);
SET_HASHTAB(env, R_NilValue);
SET_ATTRIB(env, R_NilValue);
UNPROTECT(1);
return env;
}
Oops! I forgot the definition of my simple function NewInteger:
static SEXP NewInteger(int i){
SEXP val;
PROTECT(val = NEW_INTEGER(1));
INTEGER_DATA(val)[0] = i;
UNPROTECT(1);
return val;
}
and an example that creates a new environment and then assigns a
variable named OK an integer vector length 1 with value 0:
SEXP env = NewEnv(R_GlobalEnv);
defineVar(install("OK"),NewInteger(0),env);
One comment: I would protect the env, because install() and
NewInteger() could each trigger a garbage collection. That is, use
SEXP env;
PROTECT(env = NewEnv(R_GlobalEnv));
defineVar(install("OK"),NewInteger(0),env);
UNPROTECT(1);
Duncan Murdoch
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[Rd] Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'character' & 'getEncChar' must be called on a CHARSXP
Hello,
I have list of 600K lists, each sublist a list of two elements, the
first a character, the second a list of six named elements, some
characters some numrics.
LISTA (600K) (:= h)
|__ List of two elements
|__ Character
|__ Named List of 6 elements (characters and numerics)
This works,
sip <- lapply(h,function(r) r[[2]][['sip']])
but I wish to unlist this
sip <- unlist(lapply(h,function(r) r[[2]][['sip']]))
and get the following error:
Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'list'
Debugging to find which:
i<-1
sip <- unlist(lapply(h,function(r) {
i<<-i+1 #debug messages
cat(i,"-->","\n"); print( r[[2]] ) #debug message
r[[2]][['sip']]
}))
[1]Error in print.default(r[[2]]) : 'getEncChar' must be called on a
CHARSXP
Which occurs on the 122,204'th item. All entries r[[2]] are similar so
I don't know why this happening?
The strangest thing is that this error never happened a few days ago
and the same code causes this to occur today.
Any ideas would be helpful.
Regards
Saptarshi
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Re: [Rd] Rd.sty question: LaTeX expert needed
Hi,
I would not claim I'm a latex expert ...
In the highlight package, I also use alltt environments the latex
renderer of syntax highlighted code, and I ended up masquarading a set
of character (#, \, ...) into latex boxes and then use \usebox for these
characters.
In this file :
http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/highlight/R/renderer.R?rev=168&root=highlight&view=markup
The functions boxes_latex and translator_latex might interest you. The
list of boxed characters might not be complete.
Hope this helps,
Romain
On 10/01/2009 06:50 PM, Duncan Murdoch wrote:
The Rd.sty LaTeX package is used when building the R manuals, and by the
LaTeX pages produced from the man pages.
I have tracked down some problems Gábor Csárdi was having recently (see
"Re: [R] preformatted and '#' in manual pages" in R-help) to a LaTeX
problem, and am trying to work out how to fix it.
Specifically, the .Rd file he was using had a structure like
\dQuote{
...
\preformatted{
line 1
line 2
}
}
which tools::Rd2latex in R translates to the similar LaTeX code
\dQuote{
...
\begin{alltt}
line 1
line 2
\end{alltt}
}
The problem is that the alltt environment (which is a sort of verbatim
environment, except macros are allowed) doesn't work when embedded like
this in the \dQuote{} macro. Gábor was getting errors when his line 1
contained a # symbol, and when I dealt with that, I found the formatting
was getting messed up, and the section ended up being rendered as
line 1 line 2
The \dQuote macro has a simple definition in Rd.sty as
\newcommand{\dQuote}[1]{``#1''}
so I expect the same error will happen with many other macros in Rd.sty.
So, my questions: Is there a known workaround for this in alltt?
If not, I could skip the macro expansion of \dQuote by generating the
quotes directly in Rd2latex, and most other macros could be handled
similarly. However, then nobody who uses Rd.sty would be able to
redefine the look of those macros and have things display properly.
A third possibility is that we could make it illegal to nest
\preformatted within other macros, but that seems to be an unfortunate
limitation.
Any help would be appreciated.
Duncan Murdoch
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Re: [Rd] Rd.sty question: LaTeX expert needed
On Thu, Oct 1, 2009 at 6:50 PM, Duncan Murdoch wrote:
[...]
> \dQuote{
> ...
> \preformatted{
> line 1
> line 2
> }
> }
>
[...]
Oh, there was a dQuote as well, I must be an idiot for not noticing
it. :( Anyway, for me, I will just remove the dQuote and everything
will be fine. Sorry, this is not a solution for the more general
problem
Thanks for your help,
Gabor
--
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Re: [Rd] creating environments in package's C code
Simon Urbanek wrote:
Jeff,
On Oct 1, 2009, at 12:37 , Jeff Horner wrote:
Jeff Horner wrote:
Martin Becker wrote:
Dear developers,
is it possible to create environments in C code of packages?
Simply using
SEXP env;
PROTECT (env = allocSExp(ENVSXP));
and assigning the enclosing environment with SET_ENCLOS seems to be
insufficient.
Best wishes,
Here's a function I use in rapache to create one:
static SEXP NewEnv(SEXP enclos){
SEXP env;
PROTECT(env = allocSExp(ENVSXP));
SET_FRAME(env, R_NilValue);
SET_ENCLOS(env, (enclos)? enclos: R_GlobalEnv);
SET_HASHTAB(env, R_NilValue);
SET_ATTRIB(env, R_NilValue);
UNPROTECT(1);
return env;
}
eek ... that some dangerous bit of code ;). I think Rf_NewEnviroment is
safer even if it's not the headers :P.
Interesting. I know that I patterned that function after some grepping
for ENVSXP, probably src/main/serialize.c's ReadItem() as it's similar.
Plus I only used what was available from the public headers.
So, if Rf_NewEnviroment is the right way to do it then make it public ;P.
Oops! I forgot the definition of my simple function NewInteger:
static SEXP NewInteger(int i){
SEXP val;
PROTECT(val = NEW_INTEGER(1));
INTEGER_DATA(val)[0] = i;
UNPROTECT(1);
return val;
}
I suspect you like reinventing the wheel ;). Your NewInteger is part of
the R API and is called ScalarInteger(). When you need something,
chances are that R has it already, so it's worth greping through the
headers (and sometimes even through the main sources).
Yes, that I created NewInteger is a grave oversight on my part. It's
been around since R's first release (if my svn log research was
correct). Thanks. I'm putting it on rapache's TODO list to take it out.
Jeff
Cheers,
Simon
and an example that creates a new environment and then assigns a
variable named OK an integer vector length 1 with value 0:
SEXP env = NewEnv(R_GlobalEnv);
defineVar(install("OK"),NewInteger(0),env);
Best
Jeff
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[Rd] X11 Problems
Hi all, I'm having trouble getting x11 to work with R. (This is on Debian testing.) I installed r-base and r-base-dev, and then r-cran-cairodevice. I also tried installing the Cairo package within R, which appears to work fine. This what I'm seeing: > capabilities() jpeg png tifftcltk X11 aqua http/ftp sockets TRUE TRUE TRUE TRUEFALSEFALSE TRUE TRUE libxml fifo clediticonv NLS profmemcairo TRUE TRUE TRUE TRUE TRUE TRUE TRUE > x11() Error in X11(d$display, d$width, d$height, d$pointsize, d$gamma, d$colortype, : unable to start device X11cairo In addition: Warning message: In x11() : unable to open connection to X11 display '' Any help would be appreciated! Thanks, Kay __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'character' & 'getEncChar' must be called on a CHARSXP
Saptarshi,
how did you create those lists? Can you send us the code? If not, can
you put up the .RData file? Without a reproducible example this is
hard to debug ...
Thanks,
Simon
On Oct 1, 2009, at 14:26 , Saptarshi Guha wrote:
Hello,
I have list of 600K lists, each sublist a list of two elements, the
first a character, the second a list of six named elements, some
characters some numrics.
LISTA (600K) (:= h)
|__ List of two elements
|__ Character
|__ Named List of 6 elements (characters and numerics)
This works,
sip <- lapply(h,function(r) r[[2]][['sip']])
but I wish to unlist this
sip <- unlist(lapply(h,function(r) r[[2]][['sip']]))
and get the following error:
Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'list'
Debugging to find which:
i<-1
sip <- unlist(lapply(h,function(r) {
i<<-i+1 #debug messages
cat(i,"-->","\n"); print( r[[2]] ) #debug message
r[[2]][['sip']]
}))
[1]Error in print.default(r[[2]]) : 'getEncChar' must be called on a
CHARSXP
Which occurs on the 122,204'th item. All entries r[[2]] are similar
so I don't know why this happening?
The strangest thing is that this error never happened a few days ago
and the same code causes this to occur today.
Any ideas would be helpful.
Regards
Saptarshi
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Re: [Rd] Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'character' & 'getEncChar' must be called on a CHARSXP
Hello
I could send a .Rdata file but it doesn't load throwing a similar error.
I can go through the code (below)
Now if instead of A0-A3 and B0-B3, i simply create a RAWSEXP and copy the the
raw bytes (in kvhold) return this list of two-element lists containing raw bytes
and then call
lapply(h, function(r) list(rhuz(r[[1]],r[[2]]))) #where h is what is
returned from the code below
where rhuz is a wrapper around the functions called in A0-A3, it works
So i'm quite confused here.
Thank you for your time
(R-2.9.1)
Regards
Saptarshi
//using NewList and GrowList from R sources
SEXP rv;
PROTECT( rv = NewList());
while(true){
// read an integer kvlength
// then read kvlength bytes into kvhold
// (from a file)
// The KEY
PROTECT(l = Rf_allocVector(VECSXP,2));
REXP *rexp1 = new REXP(); //A0
rexp1->ParseFromArray( kvhold, kvlength ); //A1
PROTECT(k = message2rexp(*rexp1)); //A2
delete(rexp1); //A3
SET_VECTOR_ELT( l, 0, k);
// read an integer kvlength
// then read kvlength bytes into kvhold
// (from a file)
// The VALUE
REXP *rexp2 = new REXP(); //B0
rexp2->ParseFromArray( kvhold, kvlength );//B1
PROTECT(k = message2rexp(*rexp2));//B2
delete(rexp2); //B3
SET_VECTOR_ELT( l, 1, k);
//Rf_PrintValue successfully prints both k for all k
UNPROTECT(3); // the two k's and l
rv = GrowList(rv, l);
//We break when kvlength==-1
}
//now return a list containing the objects
//similar to code in R src/main
rv = CDR(rv);
SEXP rval;
PROTECT(rval = Rf_allocVector(VECSXP, Rf_length(rv)));
for (int n = 0 ; n < LENGTH(rval) ; n++, rv = CDR(rv)){
SET_VECTOR_ELT(rval, n, CAR(rv));
}
UNPROTECT(2); //rval and rv
return(rval)
On Thu, Oct 1, 2009 at 5:36 PM, Simon Urbanek
wrote:
> Saptarshi,
>
> how did you create those lists? Can you send us the code? If not, can you
> put up the .RData file? Without a reproducible example this is hard to debug
> ...
>
> Thanks,
> Simon
>
>
> On Oct 1, 2009, at 14:26 , Saptarshi Guha wrote:
>
>> Hello,
>> I have list of 600K lists, each sublist a list of two elements, the first
>> a character, the second a list of six named elements, some characters some
>> numrics.
>> LISTA (600K) (:= h)
>> |__ List of two elements
>> |__ Character
>> |__ Named List of 6 elements (characters and numerics)
>>
>> This works,
>> sip <- lapply(h,function(r) r[[2]][['sip']])
>>
>> but I wish to unlist this
>>
>> sip <- unlist(lapply(h,function(r) r[[2]][['sip']]))
>>
>> and get the following error:
>> Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'list'
>> Debugging to find which:
>>
>> i<-1
>> sip <- unlist(lapply(h,function(r) {
>> i<<-i+1 #debug messages
>> cat(i,"-->","\n"); print( r[[2]] ) #debug message
>> r[[2]][['sip']]
>> }))
>>
>> [1]Error in print.default(r[[2]]) : 'getEncChar' must be called on a
>> CHARSXP
>>
>>
>> Which occurs on the 122,204'th item. All entries r[[2]] are similar so I
>> don't know why this happening?
>> The strangest thing is that this error never happened a few days ago and
>> the same code causes this to occur today.
>>
>>
>> Any ideas would be helpful.
>> Regards
>> Saptarshi
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>
>
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Re: [Rd] Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'character' & 'getEncChar' must be called on a CHARSXP
On Oct 1, 2009, at 6:26 PM, Saptarshi Guha wrote:
Hello
I could send a .Rdata file but it doesn't load throwing a similar
error.
That is a strong indicator that you're creating some invalid R objects
in your C code, so the problem is likely there, not in R ... The code
below is way incomplete, you can have the bug pretty much anywhere out
of sight so there is not much we can help you with...
Cheers,
Simon
I can go through the code (below)
Now if instead of A0-A3 and B0-B3, i simply create a RAWSEXP and
copy the the
raw bytes (in kvhold) return this list of two-element lists
containing raw bytes
and then call
lapply(h, function(r) list(rhuz(r[[1]],r[[2]]))) #where h is what is
returned from the code below
where rhuz is a wrapper around the functions called in A0-A3, it works
So i'm quite confused here.
Thank you for your time
(R-2.9.1)
Regards
Saptarshi
//using NewList and GrowList from R sources
SEXP rv;
PROTECT( rv = NewList());
while(true){
// read an integer kvlength
// then read kvlength bytes into kvhold
// (from a file)
// The KEY
PROTECT(l = Rf_allocVector(VECSXP,2));
REXP *rexp1 = new REXP(); //A0
rexp1->ParseFromArray( kvhold, kvlength ); //A1
PROTECT(k = message2rexp(*rexp1)); //A2
delete(rexp1); //A3
SET_VECTOR_ELT( l, 0, k);
// read an integer kvlength
// then read kvlength bytes into kvhold
// (from a file)
// The VALUE
REXP *rexp2 = new REXP(); //B0
rexp2->ParseFromArray( kvhold, kvlength );//B1
PROTECT(k = message2rexp(*rexp2));//B2
delete(rexp2); //B3
SET_VECTOR_ELT( l, 1, k);
//Rf_PrintValue successfully prints both k for all k
UNPROTECT(3); // the two k's and l
rv = GrowList(rv, l);
//We break when kvlength==-1
}
//now return a list containing the objects
//similar to code in R src/main
rv = CDR(rv);
SEXP rval;
PROTECT(rval = Rf_allocVector(VECSXP, Rf_length(rv)));
for (int n = 0 ; n < LENGTH(rval) ; n++, rv = CDR(rv)){
SET_VECTOR_ELT(rval, n, CAR(rv));
}
UNPROTECT(2); //rval and rv
return(rval)
On Thu, Oct 1, 2009 at 5:36 PM, Simon Urbanek
wrote:
Saptarshi,
how did you create those lists? Can you send us the code? If not,
can you
put up the .RData file? Without a reproducible example this is hard
to debug
...
Thanks,
Simon
On Oct 1, 2009, at 14:26 , Saptarshi Guha wrote:
Hello,
I have list of 600K lists, each sublist a list of two elements,
the first
a character, the second a list of six named elements, some
characters some
numrics.
LISTA (600K) (:= h)
|__ List of two elements
|__ Character
|__ Named List of 6 elements (characters and numerics)
This works,
sip <- lapply(h,function(r) r[[2]][['sip']])
but I wish to unlist this
sip <- unlist(lapply(h,function(r) r[[2]][['sip']]))
and get the following error:
Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'list'
Debugging to find which:
i<-1
sip <- unlist(lapply(h,function(r) {
i<<-i+1 #debug messages
cat(i,"-->","\n"); print( r[[2]] ) #debug
message
r[[2]][['sip']]
}))
[1]Error in print.default(r[[2]]) : 'getEncChar' must be called on a
CHARSXP
Which occurs on the 122,204'th item. All entries r[[2]] are
similar so I
don't know why this happening?
The strangest thing is that this error never happened a few days
ago and
the same code causes this to occur today.
Any ideas would be helpful.
Regards
Saptarshi
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Re: [Rd] Windows Laptop specification query
Thanks everyone for advice on this matter.
I've been asked to report our conclusion.
We have decide to order a duo processor(3.06GHz) Dell Precision 4400
laptop with 8GB memory and 500GB disk.
It will be running Vista 64 bit to begin with, moving over to Windows 7
once a little experience is gained with it elsewhere.
We will leave the multi CPU use of R to our larger unix servers.
cheers,
Keith
Prof Brian Ripley wrote:
The answer to (1) is in the rw-FAQ, so see
library(fortunes)
fortune('WTFM')
On Mon, 28 Sep 2009, Corrado wrote:
1) Would a package compiled for Windows 32bit run on Windows 64 bit
and use
the extended memory or not?
2) As for buying a performant laptop for R, I bought a Dell M6300 mobile
workstation which is actually portable, and installed Kubuntu 904 64 bit
alongside the standard windows installation. When I run R I only use
it in
Linux and access the data in Windows through the file system. If I
need to run
Office because some one else is sending me document to correct, I
have installed
Windows XP Pro SP3 in a virtual machine using Virtual Box, which runs
very
fairly on the M6300, and can switch it on and off whenever I need
(booting on
the virtual machine is matter of few seconds). This setup allows for
running
64 bit R on Linux (eventually compiled with -O3 -march=native by the
way, if
you feel like experimenting) which is more performant and used the
memory more
efficiently, without loosing the interacting with your windows based
colleagues.
The virtual machine can go full screen at the click of a mouse :D and
it looks
as if you were using a native Windows machine. You can install all
software
and network clients on the virtual machine. I have not booted Windows
for ages
I have been using this machine fort he last 18 months. The dual
core
works great (I chose the top processor to run simulations when I am
not in the
office), and in Linux you can control the CPU frequency. The new one
which
substitutes the M6300 is the M6400 and I would go for that possibly
(Linux
supported):
http://www1.euro.dell.com/uk/en/business/Laptops/workstation-precision-m6400-
cov/pd.aspx?refid=workstation-precision-m6400-cov&s=bsd&cs=ukbsdt1
PS: I apologise for the question on memory management but I have
never used R
on Windows but some free spirit decided to release a package only for
Windows
and only pre compiled (no sources) and I need to use it to compare
(Sorry
for the harsh comment and the rant , but I am not sure it is really
fair to
use an open source packages and programming languages for you daily
work and
make money out of it, and the first time you release something you
release it
crappy and closed source even if it is legal and allowed of
course :
( )
On Monday 28 September 2009 09:16:23 Prof Brian Ripley wrote:
On Mon, 28 Sep 2009, Sean O'Riordain wrote:
Good morning Keith,
Have a look at
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-be-
a-limit-on-the-memory-it-uses_0021
The short answer is that "it depends"...
a) memory is limited under windows
Yes, but 64-bit builds can be used on Windows -- that needs commercial
compilers and there are commercial vendors of such builds.
Even with the CRAN binary, a 64-bit version of Windows offers double
the memory over a (vanilla) 32-bit version.
b) R is essentially a serial program - HOWEVER it depends what you're
actually doing - if you're working with large matrices then there are
parallel versions of BLAS that can be used... On a multi-core windows
machine with lots of memory you can of course run up multiple
copies of R
and run each independently
There are several packages that parallelize their computations with
MPI etc, and others that help with parallelization (papply, foreach,
gputools, ). And apart from Rmpi/rpvm/snow there is also
'multicore', but not on Windows. See the R-sig-hpc list for follow up
on such issues.
As for Vista vs Windows 7, this is not the right list but Windows 7
behaves just like a version of Vista as far as we have explored it
(and the current rw-FAQ includes it and Server 2008 in the Vista
section).
Many of us have bought dual quad-core servers in the last year or so:
that includes Uwe Ligges' winbuilder machine. I suspect most of the
usage is separate R jobs running simultaneously: certainly that is the
case in my dept (where there are at least 6 8-core servers running R
jobs).
Kind regards,
Sean
On Mon, Sep 28, 2009 at 4:40 AM, Keith Satterley
wrote:
I've read some postings back in 2002/2006 about running R on multiple
core CPUs. The answer was basically separate processes work fine, but
parallelization needs to be implemented using snow/rmpi. Are the
answers
still the same?
I ask because we are about to order a laptop running Windows for a
new
staff member. Some advice on the following would be helpful.
It will be ordered with Vista, with a free upgrade to Windows 7.
It will
have 8GB of m
