[Rd] S4 Method Dispatch for Class Defined as Attribute
Hello, I am writing an interface to some functions from the CRAN package pamr, which is poorly written. I have a S4 method I declared with setMethod. I'd like to provide a signature of "pamrtrained" which is the class of object that training creates. The last two lines of code of pamr.train are : class(junk) = "pamrtrained" junk How can I dispatch on these kinds of objects, other than making the signature be "ANY" and checking the class inside the S4 method ? Might these kinds of class assignments be deprecated in a future version of R ? -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] S4 Method Dispatch for Class Defined as Attribute
Is setOldClass the solution?
e.g.
x <- list()
class(x) <- "foo"
setGeneric("bar", function(x) "bar generic")
setOldClass("foo")
setMethod("bar", "foo", function(x) "bar foo")
bar(x)
On 7 October 2014 10:00, Dario Strbenac wrote:
> Hello,
>
> I am writing an interface to some functions from the CRAN package pamr, which
> is poorly written.
>
> I have a S4 method I declared with setMethod. I'd like to provide a signature
> of "pamrtrained" which is the class of object that training creates. The last
> two lines of code of pamr.train are :
>
> class(junk) = "pamrtrained"
> junk
>
> How can I dispatch on these kinds of objects, other than making the signature
> be "ANY" and checking the class inside the S4 method ? Might these kinds of
> class assignments be deprecated in a future version of R ?
>
> --
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
>
> __
> 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] Issue installing Matrix Package
Hi, I installed R-3.1.1 on AIX-5.3 and my installation hanged up while installing Matrix Package. so i killed the gmake ; gmake install the software nad tired installing Matrix package manually - [ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1/bin/package]> /gpfs1/home/shivali/gang/R-3.1.1/bin/R CMD INSTALL Matrix the package compiled successfully but while loading Matrix package the installation hanged up - in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL" in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL" Creating a generic function for 'format' from package 'base' in package 'Matrix' Creating a generic function for 'qr.R' from package 'base' in package 'Matrix' Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix' Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix' Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix' Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix' ** help *** installing help indices ** building package indices Loading required package: Matrix On checking more i come accross the CPU utilization for thread using ps -ef command (CPU priority penalty ) is inreasing upto 120 max limit. [ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1]> ps -ef | grep R-3.1.1 shivali 323978 459010 0 14:36:14 pts/14 0:00 grep R-3.1.1 root 492034 336504 0 14:34:36 pts/11 0:00 sh /gpfs1/home/shivali/gang/R-3.1.1/lib/R/bin/Rcmd INSTALL Matrix root 525188 492034 120 14:34:37 pts/11 0:30 /gpfs1/home/shivali/gang/R-3.1.1/lib/R/bin/exec/R --args --args --args nextArgMatrix [ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1]> Please help Regards, Shivali Gangwar Email secured by Check Point __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] [R logs] Help in develop a simply logs package
Hi, With the use of R in production, it is necessary to have a system of logs effective, and light. Package exist as to futile.logger, but it require the additional coding of logs. So it is thus impossible / very difficult to use it with all package them used in the calculation Our idea is to develop one packages global, simple, who would allow to identify all the errors, warning, message generated by the functions stop(), warning() and message() stop as well as by signals and internally code, with log levels configurable later by package, functions... One way is to overwrite temporarily the functions stop(), warning() and message() of base package, but I think is not a good thing, and furthermore, we lose all signals and internally "message"... A good use of options(error) seems to do the perfect job, but only for error... Our problem / question : - At present, how it is possible to have the same features for messages and warnings? (like options(errors)) (I don't find...) - Would new options be possible in a near future R ? - Have there better / other possibilities to handle all the warnings, message of the way which we wish? Hope is clear. Open to any suggestions. Thank you in advance -- Benoit Thieurmel +33 6 69 04 06 11 DataKnowledge 46 rue Amsterdam - 75009 Paris __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R logs] Help in develop a simply logs package
On 07/10/2014, 7:04 AM, DataK - B. THIEURMEL wrote: > Hi, > > With the use of R in production, it is necessary to have a system of > logs effective, and light. > > Package exist as to futile.logger, but it require the additional coding > of logs. So it is thus impossible / very difficult to use it with all > package them used in the calculation > > Our idea is to develop one packages global, simple, who would allow to > identify all the errors, warning, message generated by the functions > stop(), warning() and message() stop as well as by signals and > internally code, with log levels configurable later by package, > functions... > > One way is to overwrite temporarily the functions stop(), warning() and > message() of base package, but I think is not a good thing, and > furthermore, we lose all signals and internally "message"... > > A good use of options(error) seems to do the perfect job, but only for > error... > > Our problem / question : > - At present, how it is possible to have the same features for messages > and warnings? (like options(errors)) (I don't find...) > - Would new options be possible in a near future R ? > - Have there better / other possibilities to handle all the warnings, > message of the way which we wish? > withCallingHandlers() lets you evaluate expressions with code to catch messages, warnings and errors. I don't know if there's a way to evaluate every expression entered at the console within withCallingHandlers() for an effect like options(error=), but you can certainly write code to read a file and evaluate every expression in it within a withCallingHandlers() call. Duncan Murdoch > Hope is clear. Open to any suggestions. > > Thank you in advance > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R logs] Help in develop a simply logs package
Thank. withCallingHandlers() and "pander::evals" seem to be very interesting, but little adapted to the analysis of one or several scripts R / of many lines of code. Our goal is one packages requiring no modifications of code R to be able to get back all the desired information. Is-there a hope in seeing R core team adding two options warn and message with the same features as options(error) ? Or if we try (and succeed) to code a patch for it, to see it integrating in R ? I think that it would be very useful. Benoit Le 2014-10-07 14:38, Gergely Daróczi a écrit : On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch wrote: On 07/10/2014, 7:04 AM, DataK - B. THIEURMEL wrote: Hi, With the use of R in production, it is necessary to have a system of logs effective, and light. Package exist as to futile.logger, but it require the additional coding of logs. So it is thus impossible / very difficult to use it with all package them used in the calculation Our idea is to develop one packages global, simple, who would allow to identify all the errors, warning, message generated by the functions stop(), warning() and message() stop as well as by signals and internally code, with log levels configurable later by package, functions... One way is to overwrite temporarily the functions stop(), warning() and message() of base package, but I think is not a good thing, and furthermore, we lose all signals and internally "message"... A good use of options(error) seems to do the perfect job, but only for error... Our problem / question : - At present, how it is possible to have the same features for messages and warnings? (like options(errors)) (I don't find...) - Would new options be possible in a near future R ? - Have there better / other possibilities to handle all the warnings, message of the way which we wish? withCallingHandlers() lets you evaluate expressions with code to catch messages, warnings and errors. That's exactly what I'm using in "pander::evals" to capture all error/warning/normal messages while evaluating an R command, and to also capture the results (as R objects), stdout and the printed version of the object -- which might be useful in a custom environment. E.g. I use this function to evaluate all R chunks in markdown document and also to store all R messages run at the rapporter.net [2] API. Please let me know if anyone is interested, and I will start cleaning up the related codebase and publish on GH -- although "pander" and "evals" is already there: https://github.com/Rapporter/pander [3] Quick demo: http://pastebin.com/jCUkgKim [4] I don't know if there's a way to evaluate every expression entered at the console within withCallingHandlers() for an effect like options(error=), but you can certainly write code to read a file and evaluate every expression in it within a withCallingHandlers() call. Duncan Murdoch Hope is clear. Open to any suggestions. Thank you in advance __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [1] Links: -- [1] https://stat.ethz.ch/mailman/listinfo/r-devel [2] http://rapporter.net [3] https://github.com/Rapporter/pander [4] http://pastebin.com/jCUkgKim -- Benoit Thieurmel +33 6 69 04 06 11 DataKnowledge 46 rue Amsterdam - 75009 Paris __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R logs] Help in develop a simply logs package
On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch wrote: > On 07/10/2014, 7:04 AM, DataK - B. THIEURMEL wrote: > > Hi, > > > > With the use of R in production, it is necessary to have a system of > > logs effective, and light. > > > > Package exist as to futile.logger, but it require the additional coding > > of logs. So it is thus impossible / very difficult to use it with all > > package them used in the calculation > > > > Our idea is to develop one packages global, simple, who would allow to > > identify all the errors, warning, message generated by the functions > > stop(), warning() and message() stop as well as by signals and > > internally code, with log levels configurable later by package, > > functions... > > > > One way is to overwrite temporarily the functions stop(), warning() and > > message() of base package, but I think is not a good thing, and > > furthermore, we lose all signals and internally "message"... > > > > A good use of options(error) seems to do the perfect job, but only for > > error... > > > > Our problem / question : > > - At present, how it is possible to have the same features for messages > > and warnings? (like options(errors)) (I don't find...) > > - Would new options be possible in a near future R ? > > - Have there better / other possibilities to handle all the warnings, > > message of the way which we wish? > > > > > withCallingHandlers() lets you evaluate expressions with code to catch > messages, warnings and errors. > That's exactly what I'm using in "pander::evals" to capture all error/warning/normal messages while evaluating an R command, and to also capture the results (as R objects), stdout and the printed version of the object -- which might be useful in a custom environment. E.g. I use this function to evaluate all R chunks in markdown document and also to store all R messages run at the rapporter.net API. Please let me know if anyone is interested, and I will start cleaning up the related codebase and publish on GH -- although "pander" and "evals" is already there: https://github.com/Rapporter/pander Quick demo: http://pastebin.com/jCUkgKim > > I don't know if there's a way to evaluate every expression entered at > the console within withCallingHandlers() for an effect like > options(error=), but you can certainly write code to read a file and > evaluate every expression in it within a withCallingHandlers() call. > > Duncan Murdoch > > > Hope is clear. Open to any suggestions. > > > > Thank you in advance > > > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R logs] Help in develop a simply logs package
On 07/10/2014 10:16 AM, DataK - B. THIEURMEL wrote: Thank. withCallingHandlers() and "pander::evals" seem to be very interesting, but little adapted to the analysis of one or several scripts R / of many lines of code. Our goal is one packages requiring no modifications of code R to be able to get back all the desired information. Is-there a hope in seeing R core team adding two options warn and message with the same features as options(error) ? Or if we try (and succeed) to code a patch for it, to see it integrating in R ? No, I don't think so. withCallingHandlers is all you need for your purpose. Duncan Murdoch I think that it would be very useful. Benoit Le 2014-10-07 14:38, Gergely Daróczi a écrit : > On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch > wrote: > >> On 07/10/2014, 7:04 AM, DataK - B. THIEURMEL wrote: >>> Hi, >>> >>> With the use of R in production, it is necessary to have a system >> of >>> logs effective, and light. >>> >>> Package exist as to futile.logger, but it require the additional >> coding >>> of logs. So it is thus impossible / very difficult to use it with >> all >>> package them used in the calculation >>> >>> Our idea is to develop one packages global, simple, who would >> allow to >>> identify all the errors, warning, message generated by the >> functions >>> stop(), warning() and message() stop as well as by signals and >>> internally code, with log levels configurable later by package, >>> functions... >>> >>> One way is to overwrite temporarily the functions stop(), >> warning() and >>> message() of base package, but I think is not a good thing, and >>> furthermore, we lose all signals and internally "message"... >>> >>> A good use of options(error) seems to do the perfect job, but >> only for >>> error... >>> >>> Our problem / question : >>> - At present, how it is possible to have the same features for >> messages >>> and warnings? (like options(errors)) (I don't find...) >>> - Would new options be possible in a near future R ? >>> - Have there better / other possibilities to handle all the >> warnings, >>> message of the way which we wish? >>> >> >> withCallingHandlers() lets you evaluate expressions with code >> to catch >> messages, warnings and errors. > > That's exactly what I'm using in "pander::evals" to capture all > error/warning/normal messages while evaluating an R command, and to > also capture the results (as R objects), stdout and the printed > version of the object -- which might be useful in a custom > environment. E.g. I use this function to evaluate all R chunks in > markdown document and also to store all R messages run at the > rapporter.net [2] API. Please let me know if anyone is interested, and > I will start cleaning up the related codebase and publish on GH -- > although "pander" and "evals" is already > there: https://github.com/Rapporter/pander [3] > > Quick demo: http://pastebin.com/jCUkgKim [4] > > >> I don't know if there's a way to evaluate every expression entered >> at >> the console within withCallingHandlers() for an effect like >> options(error=), but you can certainly write code to read a file >> and >> evaluate every expression in it within a withCallingHandlers() >> call. >> >> Duncan Murdoch >> >>> Hope is clear. Open to any suggestions. >>> >>> Thank you in advance >>> >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel [1] > > > > Links: > -- > [1] https://stat.ethz.ch/mailman/listinfo/r-devel > [2] http://rapporter.net > [3] https://github.com/Rapporter/pander > [4] http://pastebin.com/jCUkgKim __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R logs] Help in develop a simply logs package
OK, thank you for your answers. We are thus going to continue by analyzing these features Le 2014-10-07 16:29, Duncan Murdoch a écrit : On 07/10/2014 10:16 AM, DataK - B. THIEURMEL wrote: Thank. withCallingHandlers() and "pander::evals" seem to be very interesting, but little adapted to the analysis of one or several scripts R / of many lines of code. Our goal is one packages requiring no modifications of code R to be able to get back all the desired information. Is-there a hope in seeing R core team adding two options warn and message with the same features as options(error) ? Or if we try (and succeed) to code a patch for it, to see it integrating in R ? No, I don't think so. withCallingHandlers is all you need for your purpose. Duncan Murdoch I think that it would be very useful. Benoit Le 2014-10-07 14:38, Gergely Daróczi a écrit : > On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch > wrote: > >> On 07/10/2014, 7:04 AM, DataK - B. THIEURMEL wrote: >>> Hi, >>> >>> With the use of R in production, it is necessary to have a system >> of >>> logs effective, and light. >>> >>> Package exist as to futile.logger, but it require the additional >> coding >>> of logs. So it is thus impossible / very difficult to use it with >> all >>> package them used in the calculation >>> >>> Our idea is to develop one packages global, simple, who would >> allow to >>> identify all the errors, warning, message generated by the >> functions >>> stop(), warning() and message() stop as well as by signals and >>> internally code, with log levels configurable later by package, >>> functions... >>> >>> One way is to overwrite temporarily the functions stop(), >> warning() and >>> message() of base package, but I think is not a good thing, and >>> furthermore, we lose all signals and internally "message"... >>> >>> A good use of options(error) seems to do the perfect job, but >> only for >>> error... >>> >>> Our problem / question : >>> - At present, how it is possible to have the same features for >> messages >>> and warnings? (like options(errors)) (I don't find...) >>> - Would new options be possible in a near future R ? >>> - Have there better / other possibilities to handle all the >> warnings, >>> message of the way which we wish? >>> >> >> withCallingHandlers() lets you evaluate expressions with code >> to catch >> messages, warnings and errors. > > That's exactly what I'm using in "pander::evals" to capture all > error/warning/normal messages while evaluating an R command, and to > also capture the results (as R objects), stdout and the printed > version of the object -- which might be useful in a custom > environment. E.g. I use this function to evaluate all R chunks in > markdown document and also to store all R messages run at the > rapporter.net [2] API. Please let me know if anyone is interested, and > I will start cleaning up the related codebase and publish on GH -- > although "pander" and "evals" is already > there: https://github.com/Rapporter/pander [3] > > Quick demo: http://pastebin.com/jCUkgKim [4] > > >> I don't know if there's a way to evaluate every expression entered >> at >> the console within withCallingHandlers() for an effect like >> options(error=), but you can certainly write code to read a file >> and >> evaluate every expression in it within a withCallingHandlers() >> call. >> >> Duncan Murdoch >> >>> Hope is clear. Open to any suggestions. >>> >>> Thank you in advance >>> >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel [1] > > > > Links: > -- > [1] https://stat.ethz.ch/mailman/listinfo/r-devel > [2] http://rapporter.net > [3] https://github.com/Rapporter/pander > [4] http://pastebin.com/jCUkgKim -- Benoit Thieurmel +33 6 69 04 06 11 DataKnowledge 46 rue Amsterdam - 75009 Paris __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R logs] Help in develop a simply logs package
On 07/10/2014 10:41 AM, DataK - B. THIEURMEL wrote: OK, thank you for your answers. We are thus going to continue by analyzing these features The general outline would be this: 1. Call parse() on the whole file. This will catch any syntax errors. If it parses okay, you'll get a vector of expressions to evaluate. 2. Evaluate each expression in sequence within withCallingHandlers(). You need to decide what to do if you get an error(); source() would quit the script at that point, so that's probably a good idea. Duncan Murdoch Le 2014-10-07 16:29, Duncan Murdoch a écrit : > On 07/10/2014 10:16 AM, DataK - B. THIEURMEL wrote: >> Thank. withCallingHandlers() and "pander::evals" seem to be very >> interesting, but little adapted to the analysis of one or several >> scripts R / of many lines of code. Our goal is one packages requiring >> no >> modifications of code R to be able to get back all the desired >> information. >> >> Is-there a hope in seeing R core team adding two options warn and >> message with the same features as options(error) ? Or if we try (and >> succeed) to code a patch for it, to see it integrating in R ? > > No, I don't think so. withCallingHandlers is all you need for your > purpose. > > Duncan Murdoch > >> >> I think that it would be very useful. >> >> Benoit >> >> Le 2014-10-07 14:38, Gergely Daróczi a écrit : >> > On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch >> > wrote: >> > >> >> On 07/10/2014, 7:04 AM, DataK - B. THIEURMEL wrote: >> >>> Hi, >> >>> >> >>> With the use of R in production, it is necessary to have a system >> >> of >> >>> logs effective, and light. >> >>> >> >>> Package exist as to futile.logger, but it require the additional >> >> coding >> >>> of logs. So it is thus impossible / very difficult to use it with >> >> all >> >>> package them used in the calculation >> >>> >> >>> Our idea is to develop one packages global, simple, who would >> >> allow to >> >>> identify all the errors, warning, message generated by the >> >> functions >> >>> stop(), warning() and message() stop as well as by signals and >> >>> internally code, with log levels configurable later by package, >> >>> functions... >> >>> >> >>> One way is to overwrite temporarily the functions stop(), >> >> warning() and >> >>> message() of base package, but I think is not a good thing, and >> >>> furthermore, we lose all signals and internally "message"... >> >>> >> >>> A good use of options(error) seems to do the perfect job, but >> >> only for >> >>> error... >> >>> >> >>> Our problem / question : >> >>> - At present, how it is possible to have the same features for >> >> messages >> >>> and warnings? (like options(errors)) (I don't find...) >> >>> - Would new options be possible in a near future R ? >> >>> - Have there better / other possibilities to handle all the >> >> warnings, >> >>> message of the way which we wish? >> >>> >> >> >> >> withCallingHandlers() lets you evaluate expressions with code >> >> to catch >> >> messages, warnings and errors. >> > >> > That's exactly what I'm using in "pander::evals" to capture all >> > error/warning/normal messages while evaluating an R command, and to >> > also capture the results (as R objects), stdout and the printed >> > version of the object -- which might be useful in a custom >> > environment. E.g. I use this function to evaluate all R chunks in >> > markdown document and also to store all R messages run at the >> > rapporter.net [2] API. Please let me know if anyone is interested, and >> > I will start cleaning up the related codebase and publish on GH -- >> > although "pander" and "evals" is already >> > there: https://github.com/Rapporter/pander [3] >> > >> > Quick demo: http://pastebin.com/jCUkgKim [4] >> > >> > >> >> I don't know if there's a way to evaluate every expression entered >> >> at >> >> the console within withCallingHandlers() for an effect like >> >> options(error=), but you can certainly write code to read a file >> >> and >> >> evaluate every expression in it within a withCallingHandlers() >> >> call. >> >> >> >> Duncan Murdoch >> >> >> >>> Hope is clear. Open to any suggestions. >> >>> >> >>> Thank you in advance >> >>> >> >> >> >> __ >> >> R-devel@r-project.org mailing list >> >> https://stat.ethz.ch/mailman/listinfo/r-devel [1] >> > >> > >> > >> > Links: >> > -- >> > [1] https://stat.ethz.ch/mailman/listinfo/r-devel >> > [2] http://rapporter.net >> > [3] https://github.com/Rapporter/pander >> > [4] http://pastebin.com/jCUkgKim >> __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R logs] Help in develop a simply logs package
Do you think there is a way to apply a "global" withCallingHandlers() on
all environement / packages loaded, and then all R code will be executed
with the defined handler ? With this way, we can define what we want for
warning, message, error, ... one time, and apply it without needed of
parse() or added withCallingHandlers in initial code...
Something like this :
withCallingHandlersGlobal <- function(...) {
handlers <- list(...)
classes <- names(handlers)
parentenv <- all.environment
if (length(classes) != length(handlers))
stop("bad handler specification")
.Internal(.addCondHands(classes, handlers, parentenv, NULL, TRUE))
}
withCallingHandlersGlobal(warning = function(w) {print("Global
handler")})
warning("A")
"Global handler"
rnorm("A")
"Global handler"
Le 2014-10-07 16:51, Duncan Murdoch a écrit :
On 07/10/2014 10:41 AM, DataK - B. THIEURMEL wrote:
OK, thank you for your answers. We are thus going to continue by
analyzing these features
The general outline would be this:
1. Call parse() on the whole file. This will catch any syntax
errors. If it parses okay, you'll get a vector of expressions to
evaluate.
2. Evaluate each expression in sequence within withCallingHandlers().
You need to decide what to do if you get an error(); source() would
quit the script at that point, so that's probably a good idea.
Duncan Murdoch
Le 2014-10-07 16:29, Duncan Murdoch a écrit :
> On 07/10/2014 10:16 AM, DataK - B. THIEURMEL wrote:
>> Thank. withCallingHandlers() and "pander::evals" seem to be very
>> interesting, but little adapted to the analysis of one or several
>> scripts R / of many lines of code. Our goal is one packages requiring
>> no
>> modifications of code R to be able to get back all the desired
>> information.
>>
>> Is-there a hope in seeing R core team adding two options warn and
>> message with the same features as options(error) ? Or if we try (and
>> succeed) to code a patch for it, to see it integrating in R ?
>
> No, I don't think so. withCallingHandlers is all you need for your
> purpose.
>
> Duncan Murdoch
>
>>
>> I think that it would be very useful.
>>
>> Benoit
>>
>> Le 2014-10-07 14:38, Gergely Daróczi a écrit :
>> > On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch
>> > wrote:
>> >
>> >> On 07/10/2014, 7:04 AM, DataK - B. THIEURMEL wrote:
>> >>> Hi,
>> >>>
>> >>> With the use of R in production, it is necessary to have a system
>> >> of
>> >>> logs effective, and light.
>> >>>
>> >>> Package exist as to futile.logger, but it require the additional
>> >> coding
>> >>> of logs. So it is thus impossible / very difficult to use it with
>> >> all
>> >>> package them used in the calculation
>> >>>
>> >>> Our idea is to develop one packages global, simple, who would
>> >> allow to
>> >>> identify all the errors, warning, message generated by the
>> >> functions
>> >>> stop(), warning() and message() stop as well as by signals and
>> >>> internally code, with log levels configurable later by package,
>> >>> functions...
>> >>>
>> >>> One way is to overwrite temporarily the functions stop(),
>> >> warning() and
>> >>> message() of base package, but I think is not a good thing, and
>> >>> furthermore, we lose all signals and internally "message"...
>> >>>
>> >>> A good use of options(error) seems to do the perfect job, but
>> >> only for
>> >>> error...
>> >>>
>> >>> Our problem / question :
>> >>> - At present, how it is possible to have the same features for
>> >> messages
>> >>> and warnings? (like options(errors)) (I don't find...)
>> >>> - Would new options be possible in a near future R ?
>> >>> - Have there better / other possibilities to handle all the
>> >> warnings,
>> >>> message of the way which we wish?
>> >>>
>> >>
>> >> withCallingHandlers() lets you evaluate expressions with code
>> >> to catch
>> >> messages, warnings and errors.
>> >
>> > That's exactly what I'm using in "pander::evals" to capture all
>> > error/warning/normal messages while evaluating an R command, and to
>> > also capture the results (as R objects), stdout and the printed
>> > version of the object -- which might be useful in a custom
>> > environment. E.g. I use this function to evaluate all R chunks in
>> > markdown document and also to store all R messages run at the
>> > rapporter.net [2] API. Please let me know if anyone is interested, and
>> > I will start cleaning up the related codebase and publish on GH --
>> > although "pander" and "evals" is already
>> > there: https://github.com/Rapporter/pander [3]
>> >
>> > Quick demo: http://pastebin.com/jCUkgKim [4]
>> >
>> >
>> >> I don't know if there's a way to evaluate every expression entered
>> >> at
>> >> the console within withCallingHandlers() for an effect like
>> >> options(error=), but you can certainly write code to read a file
>> >> and
>> >> evaluate every expression in it within a withCallingHandlers()
>> >> call.
>> >>
>> >> Duncan Murdoch
>> >>
>> >>> Hope is clear. Open to any suggestions.
>> >>>
>> >>
Re: [Rd] [R logs] Help in develop a simply logs package
On Tue, Oct 7, 2014 at 4:51 PM, Duncan Murdoch wrote: > On 07/10/2014 10:41 AM, DataK - B. THIEURMEL wrote: > >> OK, thank you for your answers. We are thus going to continue by >> analyzing these features >> > > The general outline would be this: > > 1. Call parse() on the whole file. This will catch any syntax errors. > If it parses okay, you'll get a vector of expressions to evaluate. > > 2. Evaluate each expression in sequence within withCallingHandlers(). > You need to decide what to do if you get an error(); source() would quit > the script at that point, so that's probably a good idea. Quick demo with "pander::evals": https://gist.github.com/daroczig/480af8ad766e96dd25f4 > > > Duncan Murdoch > > >> Le 2014-10-07 16:29, Duncan Murdoch a écrit : >> > On 07/10/2014 10:16 AM, DataK - B. THIEURMEL wrote: >> >> Thank. withCallingHandlers() and "pander::evals" seem to be very >> >> interesting, but little adapted to the analysis of one or several >> >> scripts R / of many lines of code. Our goal is one packages requiring >> >> no >> >> modifications of code R to be able to get back all the desired >> >> information. >> >> >> >> Is-there a hope in seeing R core team adding two options warn and >> >> message with the same features as options(error) ? Or if we try (and >> >> succeed) to code a patch for it, to see it integrating in R ? >> > >> > No, I don't think so. withCallingHandlers is all you need for your >> > purpose. >> > >> > Duncan Murdoch >> > >> >> >> >> I think that it would be very useful. >> >> >> >> Benoit >> >> >> >> Le 2014-10-07 14:38, Gergely Daróczi a écrit : >> >> > On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch >> >> > wrote: >> >> > >> >> >> On 07/10/2014, 7:04 AM, DataK - B. THIEURMEL wrote: >> >> >>> Hi, >> >> >>> >> >> >>> With the use of R in production, it is necessary to have a system >> >> >> of >> >> >>> logs effective, and light. >> >> >>> >> >> >>> Package exist as to futile.logger, but it require the additional >> >> >> coding >> >> >>> of logs. So it is thus impossible / very difficult to use it with >> >> >> all >> >> >>> package them used in the calculation >> >> >>> >> >> >>> Our idea is to develop one packages global, simple, who would >> >> >> allow to >> >> >>> identify all the errors, warning, message generated by the >> >> >> functions >> >> >>> stop(), warning() and message() stop as well as by signals and >> >> >>> internally code, with log levels configurable later by package, >> >> >>> functions... >> >> >>> >> >> >>> One way is to overwrite temporarily the functions stop(), >> >> >> warning() and >> >> >>> message() of base package, but I think is not a good thing, and >> >> >>> furthermore, we lose all signals and internally "message"... >> >> >>> >> >> >>> A good use of options(error) seems to do the perfect job, but >> >> >> only for >> >> >>> error... >> >> >>> >> >> >>> Our problem / question : >> >> >>> - At present, how it is possible to have the same features for >> >> >> messages >> >> >>> and warnings? (like options(errors)) (I don't find...) >> >> >>> - Would new options be possible in a near future R ? >> >> >>> - Have there better / other possibilities to handle all the >> >> >> warnings, >> >> >>> message of the way which we wish? >> >> >>> >> >> >> >> >> >> withCallingHandlers() lets you evaluate expressions with code >> >> >> to catch >> >> >> messages, warnings and errors. >> >> > >> >> > That's exactly what I'm using in "pander::evals" to capture all >> >> > error/warning/normal messages while evaluating an R command, and to >> >> > also capture the results (as R objects), stdout and the printed >> >> > version of the object -- which might be useful in a custom >> >> > environment. E.g. I use this function to evaluate all R chunks in >> >> > markdown document and also to store all R messages run at the >> >> > rapporter.net [2] API. Please let me know if anyone is interested, >> and >> >> > I will start cleaning up the related codebase and publish on GH -- >> >> > although "pander" and "evals" is already >> >> > there: https://github.com/Rapporter/pander [3] >> >> > >> >> > Quick demo: http://pastebin.com/jCUkgKim [4] >> >> > >> >> > >> >> >> I don't know if there's a way to evaluate every expression entered >> >> >> at >> >> >> the console within withCallingHandlers() for an effect like >> >> >> options(error=), but you can certainly write code to read a file >> >> >> and >> >> >> evaluate every expression in it within a withCallingHandlers() >> >> >> call. >> >> >> >> >> >> Duncan Murdoch >> >> >> >> >> >>> Hope is clear. Open to any suggestions. >> >> >>> >> >> >>> Thank you in advance >> >> >>> >> >> >> >> >> >> __ >> >> >> R-devel@r-project.org mailing list >> >> >> https://stat.ethz.ch/mailman/listinfo/r-devel [1] >> >> > >> >> > >> >> > >> >> > Links: >> >> > -- >> >> > [1] https://stat.ethz.ch/mailman/listinfo/r-devel >> >> > [2] http://rapporter.net >> >> > [3] https://githu
Re: [Rd] [R logs] Help in develop a simply logs package
On 07/10/2014 11:11 AM, DataK - B. THIEURMEL wrote:
Do you think there is a way to apply a "global" withCallingHandlers() on
all environement / packages loaded, and then all R code will be executed
with the defined handler ?
That question makes no sense. withCallingHandlers is not applied to
environments or packages, it is applied to expressions.
With this way, we can define what we want for
warning, message, error, ... one time, and apply it without needed of
parse() or added withCallingHandlers in initial code...
Something like this :
withCallingHandlersGlobal <- function(...) {
handlers <- list(...)
classes <- names(handlers)
parentenv <- all.environment
if (length(classes) != length(handlers))
stop("bad handler specification")
.Internal(.addCondHands(classes, handlers, parentenv, NULL, TRUE))
}
withCallingHandlersGlobal(warning = function(w) {print("Global
handler")})
warning("A")
> "Global handler"
rnorm("A")
> "Global handler"
You would need to write the read-eval-print loop. Read text from the
console until you have a complete expression, then evaluate it in
withCallingHandlers. Repeat.
Duncan Murdoch
Le 2014-10-07 16:51, Duncan Murdoch a écrit :
> On 07/10/2014 10:41 AM, DataK - B. THIEURMEL wrote:
>> OK, thank you for your answers. We are thus going to continue by
>> analyzing these features
>
> The general outline would be this:
>
> 1. Call parse() on the whole file. This will catch any syntax
> errors. If it parses okay, you'll get a vector of expressions to
> evaluate.
>
> 2. Evaluate each expression in sequence within withCallingHandlers().
> You need to decide what to do if you get an error(); source() would
> quit the script at that point, so that's probably a good idea.
>
> Duncan Murdoch
>>
>> Le 2014-10-07 16:29, Duncan Murdoch a écrit :
>> > On 07/10/2014 10:16 AM, DataK - B. THIEURMEL wrote:
>> >> Thank. withCallingHandlers() and "pander::evals" seem to be very
>> >> interesting, but little adapted to the analysis of one or several
>> >> scripts R / of many lines of code. Our goal is one packages requiring
>> >> no
>> >> modifications of code R to be able to get back all the desired
>> >> information.
>> >>
>> >> Is-there a hope in seeing R core team adding two options warn and
>> >> message with the same features as options(error) ? Or if we try (and
>> >> succeed) to code a patch for it, to see it integrating in R ?
>> >
>> > No, I don't think so. withCallingHandlers is all you need for your
>> > purpose.
>> >
>> > Duncan Murdoch
>> >
>> >>
>> >> I think that it would be very useful.
>> >>
>> >> Benoit
>> >>
>> >> Le 2014-10-07 14:38, Gergely Daróczi a écrit :
>> >> > On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch
>> >> > wrote:
>> >> >
>> >> >> On 07/10/2014, 7:04 AM, DataK - B. THIEURMEL wrote:
>> >> >>> Hi,
>> >> >>>
>> >> >>> With the use of R in production, it is necessary to have a system
>> >> >> of
>> >> >>> logs effective, and light.
>> >> >>>
>> >> >>> Package exist as to futile.logger, but it require the additional
>> >> >> coding
>> >> >>> of logs. So it is thus impossible / very difficult to use it with
>> >> >> all
>> >> >>> package them used in the calculation
>> >> >>>
>> >> >>> Our idea is to develop one packages global, simple, who would
>> >> >> allow to
>> >> >>> identify all the errors, warning, message generated by the
>> >> >> functions
>> >> >>> stop(), warning() and message() stop as well as by signals and
>> >> >>> internally code, with log levels configurable later by package,
>> >> >>> functions...
>> >> >>>
>> >> >>> One way is to overwrite temporarily the functions stop(),
>> >> >> warning() and
>> >> >>> message() of base package, but I think is not a good thing, and
>> >> >>> furthermore, we lose all signals and internally "message"...
>> >> >>>
>> >> >>> A good use of options(error) seems to do the perfect job, but
>> >> >> only for
>> >> >>> error...
>> >> >>>
>> >> >>> Our problem / question :
>> >> >>> - At present, how it is possible to have the same features for
>> >> >> messages
>> >> >>> and warnings? (like options(errors)) (I don't find...)
>> >> >>> - Would new options be possible in a near future R ?
>> >> >>> - Have there better / other possibilities to handle all the
>> >> >> warnings,
>> >> >>> message of the way which we wish?
>> >> >>>
>> >> >>
>> >> >> withCallingHandlers() lets you evaluate expressions with code
>> >> >> to catch
>> >> >> messages, warnings and errors.
>> >> >
>> >> > That's exactly what I'm using in "pander::evals" to capture all
>> >> > error/warning/normal messages while evaluating an R command, and to
>> >> > also capture the results (as R objects), stdout and the printed
>> >> > version of the object -- which might be useful in a custom
>> >> > environment. E.g. I use this function to evaluate all R chunks in
>> >> > markdown document and also to store all R messages run at the
>> >> > rapporter.net [2] API. Please let me know if anyone is interested, and
[Rd] AIX-5.3 Issue installing Matrix Package
I've changed the subject to draw attention to this issue. For more, see inline below > Hi, > I installed R-3.1.1 on AIX-5.3 and my installation hanged up while > installing Matrix Package. > so i killed the gmake ; gmake install the software nad tired installing > Matrix package manually - > [ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1/bin/package]> > /gpfs1/home/shivali/gang/R-3.1.1/bin/R CMD INSTALL Matrix > the package compiled successfully but while loading Matrix package the > installation hanged up - > in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no > definition for class "graphNEL" > in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no > definition for class "graphNEL" > Creating a generic function for 'format' from package 'base' in package > 'Matrix' > Creating a generic function for 'qr.R' from package 'base' in package 'Matrix' > Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix' > Creating a generic function for 'qr.qy' from package 'base' in package > 'Matrix' > Creating a generic function for 'qr.qty' from package 'base' in package > 'Matrix' > Creating a generic function for 'qr.coef' from package 'base' in package > 'Matrix' > Creating a generic function for 'qr.resid' from package 'base' in package > 'Matrix' > Creating a generic function for 'qr.fitted' from package 'base' in package > 'Matrix' > ** help > *** installing help indices > ** building package indices > Loading required package: Matrix > On checking more i come accross the CPU utilization for thread using > ps -ef command (CPU priority penalty ) is inreasing upto 120 max limit. > [ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1]> ps -ef | grep R-3.1.1 > shivali 323978 459010 0 14:36:14 pts/14 0:00 grep R-3.1.1 > root 492034 336504 0 14:34:36 pts/11 0:00 sh > /gpfs1/home/shivali/gang/R-3.1.1/lib/R/bin/Rcmd INSTALL Matrix > root 525188 492034 120 14:34:37 pts/11 0:30 > /gpfs1/home/shivali/gang/R-3.1.1/lib/R/bin/exec/R --args --args --args > nextArgMatrix > [ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1]> As maintainer of the Matrix package I'm currently claiming that this is more an issue of AIX configuration when installing R (and hence the Matrix package) than an issue of the Matrix package per se. > Please help I'm trying, asking a few questions: - Have made use of the many hints and consideration about AIX installation in the official "R Administration and Installation" Manual, notably section 'C.5 AIX', see, e.g., http://cran.rstudio.org/doc/manuals/r-release/R-admin.html#AIX - What was the exact output when running /configure ? - Have you set environment variables / PATH for compilers, libraries, etc? If yes, which one? Hoping this will lead further, Martin Maechler > Regards, > Shivali Gangwar __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R logs] Help in develop a simply logs package
R has support for options(warning.expression=...), but it acts differently than the options(error=...). S (and S+) let the user override the default '.Program' expression. Its default value was essentially print(.Last.value <- eval(parse(file=stdin( but a replacement could add stuff like print the time it took to do the evaluation, put errors and warnings into a log file, or even read input expressions from an alternate source. R has some hook functions that let you do some of that, but I don't know how much they let you do. Bill Dunlap TIBCO Software wdunlap tibco.com On Tue, Oct 7, 2014 at 7:16 AM, DataK - B. THIEURMEL wrote: > Thank. withCallingHandlers() and "pander::evals" seem to be very > interesting, but little adapted to the analysis of one or several scripts R > / of many lines of code. Our goal is one packages requiring no modifications > of code R to be able to get back all the desired information. > > Is-there a hope in seeing R core team adding two options warn and message > with the same features as options(error) ? Or if we try (and succeed) to > code a patch for it, to see it integrating in R ? > > I think that it would be very useful. > > Benoit > > Le 2014-10-07 14:38, Gergely Daróczi a écrit : >> >> On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch >> wrote: >> >>> On 07/10/2014, 7:04 AM, DataK - B. THIEURMEL wrote: Hi, With the use of R in production, it is necessary to have a system >>> >>> of logs effective, and light. Package exist as to futile.logger, but it require the additional >>> >>> coding of logs. So it is thus impossible / very difficult to use it with >>> >>> all package them used in the calculation Our idea is to develop one packages global, simple, who would >>> >>> allow to identify all the errors, warning, message generated by the >>> >>> functions stop(), warning() and message() stop as well as by signals and internally code, with log levels configurable later by package, functions... One way is to overwrite temporarily the functions stop(), >>> >>> warning() and message() of base package, but I think is not a good thing, and furthermore, we lose all signals and internally "message"... A good use of options(error) seems to do the perfect job, but >>> >>> only for error... Our problem / question : - At present, how it is possible to have the same features for >>> >>> messages and warnings? (like options(errors)) (I don't find...) - Would new options be possible in a near future R ? - Have there better / other possibilities to handle all the >>> >>> warnings, message of the way which we wish? >>> >>> withCallingHandlers() lets you evaluate expressions with code >>> to catch >>> messages, warnings and errors. >> >> >> That's exactly what I'm using in "pander::evals" to capture all >> error/warning/normal messages while evaluating an R command, and to >> also capture the results (as R objects), stdout and the printed >> version of the object -- which might be useful in a custom >> environment. E.g. I use this function to evaluate all R chunks in >> markdown document and also to store all R messages run at the >> rapporter.net [2] API. Please let me know if anyone is interested, and >> I will start cleaning up the related codebase and publish on GH -- >> although "pander" and "evals" is already >> there: https://github.com/Rapporter/pander [3] >> >> Quick demo: http://pastebin.com/jCUkgKim [4] >> >> >>> I don't know if there's a way to evaluate every expression entered >>> at >>> the console within withCallingHandlers() for an effect like >>> options(error=), but you can certainly write code to read a file >>> and >>> evaluate every expression in it within a withCallingHandlers() >>> call. >>> >>> Duncan Murdoch >>> Hope is clear. Open to any suggestions. Thank you in advance >>> >>> __ >>> R-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel [1] >> >> >> >> >> Links: >> -- >> [1] https://stat.ethz.ch/mailman/listinfo/r-devel >> [2] http://rapporter.net >> [3] https://github.com/Rapporter/pander >> [4] http://pastebin.com/jCUkgKim > > > -- > Benoit Thieurmel > +33 6 69 04 06 11 > > DataKnowledge > 46 rue Amsterdam - 75009 Paris > > __ > 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
Re: [Rd] AIX-5.3 Issue installing Matrix Package
hi, >> root 492034 336504 0 14:34:36 pts/11 0:00 sh >> /gpfs1/home/shivali/gang/R-3.1.1/lib/R/bin/Rcmd INSTALL Matrix maybe sh running is not good. please install bash. CONFIG_SHELL=/boo/foo/bash before running `configure && make'. -- Best Regards, -- Eiji NAKAMA "\u4e2d\u9593\u6804\u6cbb" __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
