[Rd] Small nit in Sweave
Two small Sweave issues. 1. I had the following line in my code echo=FALSE, results=hide resulting in the message Error in match.arg(options$results, c(verbatim, tex, hide)) : 'arg' should be one of “verbatim”, “tex”, “hide” I puzzled on this a bit since my argument exactly matched the message, until I thought of trying it without the quotes. 2. Where should I have reported this? Sweave is not on CRAN so I couldn't find the maintainer email there. Perhaps I'm missing something obvious though Terry T. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Small nit in Sweave
On Nov 15, 2011, at 1:10 PM, Terry Therneau wrote: Two small Sweave issues. 1. I had the following line in my code echo=FALSE, results=hide resulting in the message Error in match.arg(options$results, c(verbatim, tex, hide)) : 'arg' should be one of “verbatim”, “tex”, “hide” I puzzled on this a bit since my argument exactly matched the message, until I thought of trying it without the quotes. 2. Where should I have reported this? Sweave is not on CRAN so I couldn't find the maintainer email there. Perhaps I'm missing something obvious though Terry T. Interesting. I never thought of using the 'results' options as quoted character vectors, even though in ?RweaveLatex, the description for the 'results' options indicates: character string (verbatim). If verbatim, the output of R commands is included in the verbatim-like Soutput environment. If tex, the output is taken to be already proper LaTeX markup and included as is. If hide then all output is completely suppressed (but the code executed during the weave). I can see how that could be confusing. All examples of the chunk headers I have seen do not use quoted values. Perhaps the above should state Non-quoted character values or similar verbiage. In terms of reporting Terry, Sweave is in the 'utils' package, which is part of Base R, therefore under the copyright of The R Foundation. So here is fine. Regards, Marc Schwartz __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question on parsing R code from C
Simon Urbanek simon.urbanek at r-project.org writes: AFAIR you have to evaluate parse(text=...) for that, there is no C-level access to parser errors. Yes that did it, thanks! If you get a crash, you're not setting up you R correctly. If your R quits then you are in non-interactive mode and you didn't setup an error handler. I am really getting a crash for strings with incorrect escapes like when evaluating: parse(text='ggsave(C:\test.png)') Using R.exe does not result in a crash. It's really puzzling that all the other parse errors (like rnorm(10a10)) or evaluation errors (like idontexists(10)) correctly results in an error string an no crash. Code that executes correctly works fine as well. Do you have any suggestion on what may be causing the issue? I am initializing R with: Rf_initEmbeddedR passing progsname, --vanilla and --slave And I am parsing/evaluating with: Rf_mkString (protected) passing capture.output(eval(parse(text=code))) (I also tried with allocVector + Rf_mkChar with no difference) Followed by: R_ParseVector(r_cmd, -1, parse_err, R_NilValue) (protected) with r_cmd given by the SEXP returned above And by: R_tryEvalSilent(VECTOR_ELT(r_expr,i), R_GlobalEnv, eval_err) (protected) iterating along r_expr which is given by the SEXP returned above. I don't perform any other operation at all. R_Interactive is true. I prefer using Rf_eval() and try(..., silent=TRUE) - you can check on the class of the result to see if there was an error. I actually find it easier (less code) to use R_tryEvalSilent followed by R_curErrorBuf in case of error. Are they going to be deprecated? BTW: you are asking a lot of questions the are answered in the Rserve FAQ (since what you do is exactly what Rserve provides) so you may want to have a quick look: http://rforge.net/Rserve/faq.html Thanks a lot, that helped as well! Plotting works as well but after the window is created it freezes, cannot be closed without passing dev.off() command. I understand this is expected behavior and that it cannot be changed using Rf_initEmbeddedR and Rf_endEmbeddedR. The only problem I am having (aside from the wrongly escaped string crashes) is that if I call: Rf_initEmbeddedR (to open the global R state) followed by Rf_endEmbeddedR (to close the global R state) and then I try to open the global state again with Rf_initEmbeddedR I get: Lost warning messages on stderr and calling other R functions result in hang. What am I doing wrong? Thanks a lot for all the suggestions so far, I have made a lot of progress. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] When collected warnings exceeds 50
On Thu, Nov 10, 2011 at 11:00 PM, Jeffrey Horner
jeffrey.hor...@gmail.com wrote:
On Thu, Nov 10, 2011 at 10:54 PM, Jeffrey Horner
jeffrey.hor...@gmail.com wrote:
Hi,
I've been tracking down a memory leak in an rApache application,
http://data.vanderbilt.edu/rapache/bbplot. The code was deployed in
2007 and has survived numerous upgrades of both R and rApache
(including upgrades and bugs in RMySQL). It's written in such a way so
that web crawlers will download every possible URL the app will
create. It's not a high-traffic app, but just about every line of code
is executed at some point during a crawl by Google, Bing, etc.
Here's the salient point: the app (well, just about all rApache apps)
sets option warn to 0 to collect all warnings until a request is
completed. It turns out that some requests will collect more than 50
warnings, and the result is an apache process that leaks memory until
finally seg faulting somewhere in one of R's extra packages, if I
recall correctly.
After what seems like a month working on this problem, I think I've
narrowed it down to a simple test case. I'm testing with R-devel
r57624 on ubuntu linux. Running the following under valgrind:
R -d valgrind
options(warn=0)
for (i in 1:51) factor(1,levels=c(1,1) # duplicate level warningcall
Missed a closing parenthesis. should be :
options(warn=0)
for (i in 1:51) factor(1,levels=c(1,1)) # duplicate level warningcall
and you should see Invalid read messages. I've narrowed it down to
vwarningcall_dflt starting a new R context via begincontext() but
returning early without calling endcontext() in errors.c:
svn diff src/main/errors.c
Index: src/main/errors.c
===
--- src/main/errors.c (revision 57624)
+++ src/main/errors.c (working copy)
@@ -333,8 +333,11 @@
char *tr; int nc;
if(!R_CollectWarnings)
setupwarnings();
- if( R_CollectWarnings 49 )
+ if( R_CollectWarnings 49 ) {
+ endcontext(cntxt);
+ inWarning = 0;
return;
+ }
SET_VECTOR_ELT(R_Warnings, R_CollectWarnings, call);
Rvsnprintf(buf, min(BUFSIZE, R_WarnLength+1), format, ap);
if(R_WarnLength BUFSIZE - 20 strlen(buf) == R_WarnLength)
This fix eliminates the Invalid read errors, but I'm unsure if it
fixes my application. I'll find out tomorrow.
The memory leak was occurring in the Cairo package and it is fixed
now, but the issue I spelled out above is still a concern.
Jeff
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Re: [Rd] Question on parsing R code from C
On Nov 15, 2011, at 5:39 PM, KR wrote: Simon Urbanek simon.urbanek at r-project.org writes: AFAIR you have to evaluate parse(text=...) for that, there is no C-level access to parser errors. Yes that did it, thanks! If you get a crash, you're not setting up you R correctly. If your R quits then you are in non-interactive mode and you didn't setup an error handler. I am really getting a crash for strings with incorrect escapes like when evaluating: parse(text='ggsave(C:\test.png)') Using R.exe does not result in a crash. It's really puzzling that all the other parse errors (like rnorm(10a10)) or evaluation errors (like idontexists(10)) correctly results in an error string an no crash. Code that executes correctly works fine as well. Do you have any suggestion on what may be causing the issue? Not without seeing the actual code. (And details such as which platform you're on). Note that setup_Rmainloop() is the last to set the SETJMP context target so you should make sure the stack is still present after it finished (i.e. you can't call it from a sub-function - which Rf_initEmbeddedR does) otherwise error without an enclosing context will crash. Or to put it other way round, create a context around your parse/eval code (probably the easiest way to do that is to use R_ToplevelExec). I am initializing R with: Rf_initEmbeddedR passing progsname, --vanilla and --slave And I am parsing/evaluating with: Rf_mkString (protected) passing capture.output(eval(parse(text=code))) (I also tried with allocVector + Rf_mkChar with no difference) Followed by: R_ParseVector(r_cmd, -1, parse_err, R_NilValue) (protected) with r_cmd given by the SEXP returned above And by: R_tryEvalSilent(VECTOR_ELT(r_expr,i), R_GlobalEnv, eval_err) (protected) iterating along r_expr which is given by the SEXP returned above. I don't perform any other operation at all. R_Interactive is true. I prefer using Rf_eval() and try(..., silent=TRUE) - you can check on the class of the result to see if there was an error. I actually find it easier (less code) to use R_tryEvalSilent followed by R_curErrorBuf in case of error. Are they going to be deprecated? BTW: you are asking a lot of questions the are answered in the Rserve FAQ (since what you do is exactly what Rserve provides) so you may want to have a quick look: http://rforge.net/Rserve/faq.html Thanks a lot, that helped as well! Plotting works as well but after the window is created it freezes, cannot be closed without passing dev.off() command. I understand this is expected behavior and that it cannot be changed using Rf_initEmbeddedR and Rf_endEmbeddedR. The only problem I am having (aside from the wrongly escaped string crashes) is that if I call: Rf_initEmbeddedR (to open the global R state) followed by Rf_endEmbeddedR (to close the global R state) and then I try to open the global state again with Rf_initEmbeddedR I get: Lost warning messages on stderr and calling other R functions result in hang. What am I doing wrong? Nothing. You can initialize R only once. Cheers, Simon Thanks a lot for all the suggestions so far, I have made a lot of progress. __ 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
