[Rd] Dealing with R list objects in C/C++
Hi, I'd like to construct an R list object in C++, fill it with relevant data, and pass it to an R function which will return a different list object back. I have browsed through all the R manuals, and examples under tests/Embedding, but can't figure out the correct way. Below is my code snippet: #include // Rf_initEmbeddedR and other setups already performed SEXP arg, ret; // this actually creates a pairlist. I can't find any API that creates a list PROTECT(arg = allocList(3)); // I want the first element to be type integer, second double, and third a vector. INTEGER(arg)[0] = 1;// <- runtime exception: "INTEGER() can only be applied to a 'integer', not a 'pairlist' REAL(arg)[1] = 2.5; // control never reached here VECTOR_PTR(arg)[2] = allocVector(REALSXP, 4); REAL(VECTOR_PTR(arg)[2])[0] = 10.0; REAL(VECTOR_PTR(arg)[2])[1] = 11.0; REAL(VECTOR_PTR(arg)[2])[2] = 12.0; REAL(VECTOR_PTR(arg)[2])[3] = 13.0; PROTECT(call = lang2(install(entryPoint.c_str()), arg)); ret = R_tryEval(call, R_GlobalEnv, &errorOccurred); I'll be grateful if you can point me to any online docs/samples. Thanks in advance, Wayne ___ This e-mail may contain information that is confidential, privileged or otherwise protected from disclosure. If you are not an intended recipient of this e-mail, do not duplicate or redistribute it by any means. Please delete it and any attachments and notify the sender that you have received it in error. Unless specifically indicated, this e-mail is not an offer to buy or sell or a solicitation to buy or sell any securities, investment products or other financial product or service, an official confirmation of any transaction, or an official statement of Barclays. Any views or opinions presented are solely those of the author and do not necessarily represent those of Barclays. This e-mail is subject to terms available at the following link: www.barcap.com/emaildisclaimer. By messaging with Barclays you consent to the foregoing. Barclays Capital is the investment banking division of Barclays Bank PLC, a company registered in England (number 1026167) with its registered offi! ce at 1 Churchill Place, London, E14 5HP. This email may relate to or be sent from other members of the Barclays Group. ___ [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Dealing with R list objects in C/C++
Many thanks for the quick reply Martin, your code works as expected. Next I'd
like to retrieve heterogeneous data from an SEXP object (let's just pretend
it's the same type as the one what I'm constructing). I'm sure the relevant
APIs are defined in Rinternals.h, do we have API documentations for this header
file somewhere?
@Dirk: thanks for your help too. I'm doing something very simple at the
moment, so I prefer not to bring in Rinside/Rcpp if possible.
Thanks again,
Wayne
-Original Message-
From: Martin Morgan [mailto:mtmor...@fhcrc.org]
Sent: Wednesday, January 26, 2011 10:04 PM
To: Zhang, Wayne: IT (NYK)
Cc: r-devel@r-project.org
Subject: Re: [Rd] Dealing with R list objects in C/C++
On 01/26/2011 02:56 PM, wayne.zh...@barclayscapital.com wrote:
> Hi,
>
> I'd like to construct an R list object in C++, fill it with relevant data,
> and pass it to an R function which will return a different list object back.
> I have browsed through all the R manuals, and examples under tests/Embedding,
> but can't figure out the correct way. Below is my code snippet:
>
> #include
> // Rf_initEmbeddedR and other setups already performed
>
> SEXP arg, ret;
>
> // this actually creates a pairlist. I can't find any API that creates a
> list
> PROTECT(arg = allocList(3));
Allocate a list of length 3 via SEXPTYPE VECSXP
PROTECT(arg = allocVector(VECSXP, 3));
>
> // I want the first element to be type integer, second double, and third a
> vector.
> INTEGER(arg)[0] = 1;// <- runtime exception: "INTEGER() can
> only be applied to a 'integer', not a 'pairlist'
set the first element of the list to an integer vector of length 1, and
assign a value
SET_VECTOR_ELT(arg, 0, allocVector(INTSXP, 1));
INTEGER(VECTOR_ELT(arg, 0))[0] = 1
or more succinctly
SET_VECTOR_ELT(arg, 0, ScalarInteger(1));
> REAL(arg)[1] = 2.5; // control never reached here
and the second element
SET_VECTOR_ELT(arg, 1, ScalarReal(2.5));
> VECTOR_PTR(arg)[2] = allocVector(REALSXP, 4);
and for the third allocate a REALSXP and then fill
SET_VECTOR_ELT(arg, 2, allocVector(REALSXP, 4));
next lines should be ok as REAL(VECTOR_ELT(arg, 2))[0] = 10.0; or with
less typing as
double *x = REAL(VECTOR_ETL(arg, 2));
x[0] = 10.0; x[1] = 11.0; x[2] = 12.0; x[3] = 13.0;
> REAL(VECTOR_PTR(arg)[2])[0] = 10.0;
> REAL(VECTOR_PTR(arg)[2])[1] = 11.0;
> REAL(VECTOR_PTR(arg)[2])[2] = 12.0;
> REAL(VECTOR_PTR(arg)[2])[3] = 13.0;
>
> PROTECT(call = lang2(install(entryPoint.c_str()), arg));
not sure where entryPoint.c_str() is coming from, but
PROTECT(call = lang2(install("fun"), arg));
with some debate about whether install("fun") should be PROTECT'ed.
>
> ret = R_tryEval(call, R_GlobalEnv, &errorOccurred);
likely PROTECT(ret = ...) while checking errorOccurred, etc.
Hope that helps,
Martin
>
>
> I'll be grateful if you can point me to any online docs/samples.
>
> Thanks in advance,
> Wayne
>
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i!
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[Rd] How to disable R's crash prompt
Dear R devel, I have a C++ app that calls into embedded R to perform some analytic calculations. When my app encounters a segmentation fault, R always prints the following crash prompt and asks me to enter an action: *** caught segfault *** address 0x8, cause 'memory not mapped' Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace The problem is my app will be run in non-interactive mode, so there is no way for me to enter the action. Is there a way to disable the crash prompt and have R simply crash the whole app? I have tried using "-file=/dev/null", "-slave", "-vanilla", and pretty much all other start options, to no avail. Thanks in advance for your help, Wayne ___ This e-mail may contain information that is confidential, privileged or otherwise protected from disclosure. If you are not an intended recipient of this e-mail, do not duplicate or redistribute it by any means. Please delete it and any attachments and notify the sender that you have received it in error. Unless specifically indicated, this e-mail is not an offer to buy or sell or a solicitation to buy or sell any securities, investment products or other financial product or service, an official confirmation of any transaction, or an official statement of Barclays. Any views or opinions presented are solely those of the author and do not necessarily represent those of Barclays. This e-mail is subject to terms available at the following link: www.barcap.com/emaildisclaimer. By messaging with Barclays you consent to the foregoing. Barclays Capital is the investment banking division of Barclays Bank PLC, a company registered in England (number 1026167) with its registered offi! ce at 1 Churchill Place, London, E14 5HP. This email may relate to or be sent from other members of the Barclays Group. ___ [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] How to disable R's crash prompt
Thanks for your quick comment Mr. Ripley. I'm a newbie in R so excuse me for
not knowing the obvious. Could you elaborate on what code I should look at,
and what documentation I should go to?
This is my C++ code on calling embedded R (on redhat enterprise linux 4):
char *localArgs[] = { "R", "--silent" }; // tried --slave, -f, --vanilla
too
Rf_initEmbeddedR(sizeof(localArgs)/sizeof(localArgs[0]), localArgs);
PROTECT(load = lang2(install("source"), mkString(file.c_str(; // file
contains R code
R_tryEval(load, R_GlobalEnv, &errorOccurred);
PROTECT(call = lang2(install(entryPoint.c_str()), input));// entry
point is an R function defined in "file" above
PROTECT(output = R_tryEval(call, R_GlobalEnv, &errorOccurred));
UNPROTECT(3);
What should I do in C++ to make R non-interactive?
Thanks,
Wayne
-Original Message-
From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk]
Sent: Tuesday, March 08, 2011 9:51 AM
To: Zhang, Wayne: IT (NYK)
Cc: r-devel@r-project.org
Subject: Re: [Rd] How to disable R's crash prompt
On Tue, 8 Mar 2011, wayne.zh...@barclayscapital.com wrote:
> Dear R devel,
>
> I have a C++ app that calls into embedded R to perform some analytic
> calculations. When my app encounters a segmentation fault, R always
> prints the following crash prompt and asks me to enter an action:
>
>
> *** caught segfault ***
> address 0x8, cause 'memory not mapped'
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
>
>
> The problem is my app will be run in non-interactive mode, so there
> is no way for me to enter the action. Is there a way to disable the
R does not do that in 'non-interactive mode'. Take a look at the
code: that section is conditional on R_Interactive.
> crash prompt and have R simply crash the whole app? I have tried
> using "-file=/dev/null", "-slave", "-vanilla", and pretty much all
> other start options, to no avail.
They do not control if R is interactive: the front-end (yours, I
presume since you mention embedding but do not otherwise give any
details) does.
> Thanks in advance for your help,
>
> Wayne
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
___
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Re: [Rd] How to disable R's crash prompt
Hi Dirk,
My code on calling embedded R from C++ is attached in the other mail.
As you see, I'm not using RInside. My app already works (except when it seg
faults) so I prefer not to change it.
Thanks,
Wayne
-Original Message-
From: Dirk Eddelbuettel [mailto:e...@debian.org]
Sent: Tuesday, March 08, 2011 10:10 AM
To: Zhang, Wayne: IT (NYK)
Cc: r-devel@r-project.org
Subject: Re: [Rd] How to disable R's crash prompt
On 8 March 2011 at 09:24, wayne.zh...@barclayscapital.com wrote:
| Dear R devel,
|
| I have a C++ app that calls into embedded R to perform some analytic
calculations. When my app encounters a segmentation fault, R always prints the
following crash prompt and asks me to enter an action:
|
|
| *** caught segfault ***
| address 0x8, cause 'memory not mapped'
|
| Possible actions:
| 1: abort (with core dump, if enabled)
| 2: normal R exit
| 3: exit R without saving workspace
| 4: exit R saving workspace
|
|
|
| The problem is my app will be run in non-interactive mode, so there is no way
for me to enter the action. Is there a way to disable the crash prompt and
have R simply crash the whole app? I have tried using "-file=/dev/null",
"-slave", "-vanilla", and pretty much all other start options, to no avail.
Are you using RInside? You could try rebuilding it with the this (from
src/RInside.cpp) set to true
bool verbose = false;
as well as with possibly more debugging output added to the RInside
destructor (where I removed a few commented-out lines for brevity):
RInside::~RInside() { // now empty as MemBuf is internal
logTxt("RInside::dtor BEGIN", verbose);
R_dot_Last();
R_RunExitFinalizers();
R_CleanTempDir();
Rf_endEmbeddedR(0);
logTxt("RInside::dtor END", verbose);
instance_ = 0 ;
}
to at least confirm that you get here. And if you really,really wanted to I
suppose you could try to do without some of these cleanup and finalizer
functions. But I think that would send you into somewhat uncharted territory,
so you probably want to do read Section 8.1 ("8.1 Embedding R under
Unix-alikes") of Writing R Extension carefully. Best bet may still be to
avoid the segfault alltogether if you can.
Hope this helps, Dirk
--
Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com
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e-mail is subject to terms available at the following link:
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Re: [Rd] How to disable R's crash prompt
That did the trick. Thank you soo much Simon!
Wayne
-Original Message-
From: Simon Urbanek [mailto:simon.urba...@r-project.org]
Sent: Tuesday, March 08, 2011 5:28 PM
To: Zhang, Wayne: IT (NYK)
Cc: rip...@stats.ox.ac.uk; r-devel@r-project.org
Subject: Re: [Rd] How to disable R's crash prompt
On Mar 8, 2011, at 10:01 AM,
wrote:
> Thanks for your quick comment Mr. Ripley. I'm a newbie in R so excuse me for
> not knowing the obvious. Could you elaborate on what code I should look at,
> and what documentation I should go to?
>
> This is my C++ code on calling embedded R (on redhat enterprise linux 4):
>
>char *localArgs[] = { "R", "--silent" }; // tried --slave, -f, --vanilla
> too
>Rf_initEmbeddedR(sizeof(localArgs)/sizeof(localArgs[0]), localArgs);
>
R_Interactive = FALSE;
>PROTECT(load = lang2(install("source"), mkString(file.c_str(; // file
> contains R code
>R_tryEval(load, R_GlobalEnv, &errorOccurred);
>
>PROTECT(call = lang2(install(entryPoint.c_str()), input));// entry
> point is an R function defined in "file" above
>PROTECT(output = R_tryEval(call, R_GlobalEnv, &errorOccurred));
>
>UNPROTECT(3);
>
>
> What should I do in C++ to make R non-interactive?
>
> Thanks,
> Wayne
>
>
> -Original Message-
> From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk]
> Sent: Tuesday, March 08, 2011 9:51 AM
> To: Zhang, Wayne: IT (NYK)
> Cc: r-devel@r-project.org
> Subject: Re: [Rd] How to disable R's crash prompt
>
> On Tue, 8 Mar 2011, wayne.zh...@barclayscapital.com wrote:
>
>> Dear R devel,
>>
>> I have a C++ app that calls into embedded R to perform some analytic
>> calculations. When my app encounters a segmentation fault, R always
>> prints the following crash prompt and asks me to enter an action:
>>
>>
>> *** caught segfault ***
>> address 0x8, cause 'memory not mapped'
>>
>> Possible actions:
>> 1: abort (with core dump, if enabled)
>> 2: normal R exit
>> 3: exit R without saving workspace
>> 4: exit R saving workspace
>>
>>
>>
>> The problem is my app will be run in non-interactive mode, so there
>> is no way for me to enter the action. Is there a way to disable the
>
> R does not do that in 'non-interactive mode'. Take a look at the
> code: that section is conditional on R_Interactive.
>
>> crash prompt and have R simply crash the whole app? I have tried
>> using "-file=/dev/null", "-slave", "-vanilla", and pretty much all
>> other start options, to no avail.
>
> They do not control if R is interactive: the front-end (yours, I
> presume since you mention embedding but do not otherwise give any
> details) does.
>
>> Thanks in advance for your help,
>>
>> Wayne
>
> --
> Brian D. Ripley, rip...@stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UKFax: +44 1865 272595
> ___
>
> This e-mail may contain information that is confidential, privileged or
> otherwise protected from disclosure. If you are not an intended recipient of
> this e-mail, do not duplicate or redistribute it by any means. Please delete
> it and any attachments and notify the sender that you have received it in
> error. Unless specifically indicated, this e-mail is not an offer to buy or
> sell or a solicitation to buy or sell any securities, investment products or
> other financial product or service, an official confirmation of any
> transaction, or an official statement of Barclays. Any views or opinions
> presented are solely those of the author and do not necessarily represent
> those of Barclays. This e-mail is subject to terms available at the following
> link: www.barcap.com/emaildisclaimer. By messaging with Barclays you consent
> to the foregoing. Barclays Capital is the investment banking division of
> Barclays Bank PLC, a company registered in England (number 1026167) with its
> registered of!
fi!
> ce at 1 Churchill Place, London, E14 5HP. This email may relate to or be
> sent from other members of the Barclays Group.
>
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Re: [Rd] How to disable R's crash prompt
I never said I wasn't going to fix the bug, and believe me big banks do want their apps to be of high quality, but until the bugs are fixed I want my app to die instead of becoming a zombie. But thanks for your opinion and all others that offered help along the way. Wayne -Original Message- From: b.rowling...@googlemail.com [mailto:b.rowling...@googlemail.com] On Behalf Of Barry Rowlingson Sent: Wednesday, March 09, 2011 5:26 AM To: Zhang, Wayne: IT (NYK) Cc: simon.urba...@r-project.org; rip...@stats.ox.ac.uk; r-devel@r-project.org Subject: Re: [Rd] How to disable R's crash prompt On Tue, Mar 8, 2011 at 10:41 PM, wrote: > That did the trick. Thank you soo much Simon! But really you *should* fix the segfault. Either you know why it happens, in which case you should spot it before it happens and do something sensible, or you don't know why it happens, in which case it could be a serious bug in your code. Even if you *do* know why it happens, there may be other bugs in your code that cause segfaults that you *dont* know about, and you'll miss them because you are stupidly ignoring all segfaults. Fix the bugs. Barry ___ This e-mail may contain information that is confidential, privileged or otherwise protected from disclosure. If you are not an intended recipient of this e-mail, do not duplicate or redistribute it by any means. Please delete it and any attachments and notify the sender that you have received it in error. Unless specifically indicated, this e-mail is not an offer to buy or sell or a solicitation to buy or sell any securities, investment products or other financial product or service, an official confirmation of any transaction, or an official statement of Barclays. Any views or opinions presented are solely those of the author and do not necessarily represent those of Barclays. This e-mail is subject to terms available at the following link: www.barcap.com/emaildisclaimer. By messaging with Barclays you consent to the foregoing. Barclays Capital is the investment banking division of Barclays Bank PLC, a company registered in England (number 1026167) with its registered office at 1 Churchill Place, London, E14 5HP. This email may relate to or be sent from other members of the Barclays Group. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
