From thosjleeper at gmail.com  Wed Oct  8 12:49:19 2014
From: thosjleeper at gmail.com (Thomas J. Leeper)
Date: Wed, 8 Oct 2014 12:49:19 +0200
Subject: [Rd] [R logs] Help in develop a simply logs package
Message-ID: <CAOC91MTyeLS2oAS7fd3FNJbk+RReMtutw_QPwJom497qUyfMAg@mail.gmail.com>

Maybe this isn't what you're going for, but to implement the
"ritesink" widget in my package rite (which is a colored tcltk widget
to display output, messages, warnings, and errors), I use a
combination of `sink`, `addTaskCallback`, and a modification of
`options("error")`. In short, the task callback is executed after
every top-level evaluation. The function in that callback reads
contents from `sink`ed output and message streams and, if anything new
has been added to either, it writes those contents to the widget. The
custom error handler similarly writes to the widget instead of the
console. Following this design, instead of writing to the widget, you
could write all of that to some kind of formatted log file.

The package is on CRAN and you can take quick look at the source code
on GitHub: https://github.com/leeper/rite/blob/master/R/ritesink.r

Thomas J. Leeper
http://www.thomasleeper.com


On Wed, Oct 8, 2014 at 12:00 PM,  <r-devel-request at r-project.org> wrote:
> Message: 2
> Date: Tue, 07 Oct 2014 13:04:34 +0200
> From: "DataK - B. THIEURMEL" <bt at datak.fr>
> To: r-devel at r-project.org
> Subject: [Rd] [R logs] Help in develop a simply logs package
> Message-ID: <4726f6636a227512e8a3ec4ae1562e73 at datak.fr>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> 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
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 07 Oct 2014 08:21:36 -0400
> From: Duncan Murdoch <murdoch.duncan at gmail.com>
> To: "DataK - B. THIEURMEL" <bt at datak.fr>, r-devel at r-project.org
> Subject: Re: [Rd] [R logs] Help in develop a simply logs package
> Message-ID: <5433DAD0.8080305 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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
>>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 07 Oct 2014 16:16:53 +0200
> From: "DataK - B. THIEURMEL" <bt at datak.fr>
> To: Gergely Dar?czi <daroczig at rapporter.net>
> Cc: r-devel at r-project.org
> Subject: Re: [Rd] [R logs] Help in develop a simply logs package
> Message-ID: <50055615b4a67b88787ba18dc0c607b8 at datak.fr>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> 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 Dar?czi a ?crit?:
>> On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch
>> <murdoch.duncan at gmail.com> 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 at 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
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 7 Oct 2014 14:38:50 +0200
> From: Gergely Dar?czi <daroczig at rapporter.net>
> To: Duncan Murdoch <murdoch.duncan at gmail.com>
> Cc: r-devel at r-project.org
> Subject: Re: [Rd] [R logs] Help in develop a simply logs package
> Message-ID:
>         <CAPvvxJV=P4Hj3hL+cic2XN1CRtH5BrQROZHb8AHWY501Pq5FBw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch <murdoch.duncan at gmail.com>
> 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 at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>         [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 07 Oct 2014 10:29:48 -0400
> From: Duncan Murdoch <murdoch.duncan at gmail.com>
> To: "DataK - B. THIEURMEL" <bt at datak.fr>, Gergely Dar?czi
>         <daroczig at rapporter.net>
> Cc: r-devel at r-project.org
> Subject: Re: [Rd] [R logs] Help in develop a simply logs package
> Message-ID: <5433F8DC.8040009 at gmail.com>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> 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 Dar?czi a ?crit :
>> > On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch
>> > <murdoch.duncan at gmail.com> 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 at 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
>>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 07 Oct 2014 16:41:05 +0200
> From: "DataK - B. THIEURMEL" <bt at datak.fr>
> To: Duncan Murdoch <murdoch.duncan at gmail.com>
> Cc: r-devel at r-project.org
> Subject: Re: [Rd] [R logs] Help in develop a simply logs package
> Message-ID: <e630f94c1003f37cc1eb9a47ff8b5152 at datak.fr>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> 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 ?crit?:
>> 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 Dar?czi a ?crit :
>>> > On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch
>>> > <murdoch.duncan at gmail.com> 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 at 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
>
>
>
> ------------------------------
>
> Message: 8
> Date: Tue, 07 Oct 2014 10:51:44 -0400
> From: Duncan Murdoch <murdoch.duncan at gmail.com>
> To: "DataK - B. THIEURMEL" <bt at datak.fr>
> Cc: r-devel at r-project.org
> Subject: Re: [Rd] [R logs] Help in develop a simply logs package
> Message-ID: <5433FE00.3090605 at gmail.com>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> 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 ?crit :
>> > 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 Dar?czi a ?crit :
>> >> > On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch
>> >> > <murdoch.duncan at gmail.com> 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 at 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
>> >>
>>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Tue, 07 Oct 2014 17:11:08 +0200
> From: "DataK - B. THIEURMEL" <bt at datak.fr>
> To: Duncan Murdoch <murdoch.duncan at gmail.com>
> Cc: r-devel at r-project.org
> Subject: Re: [Rd] [R logs] Help in develop a simply logs package
> Message-ID: <a5c4d7cbc69d368488567170490b8e2d at datak.fr>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> 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 ?crit?:
>> 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 ?crit :
>>> > 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 Dar?czi a ?crit :
>>> >> > On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch
>>> >> > <murdoch.duncan at gmail.com> 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 at 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
>
>
>
> ------------------------------
>
> Message: 10
> Date: Tue, 7 Oct 2014 18:05:03 +0200
> From: Gergely Dar?czi <daroczig at rapporter.net>
> To: Duncan Murdoch <murdoch.duncan at gmail.com>
> Cc: r-devel at r-project.org
> Subject: Re: [Rd] [R logs] Help in develop a simply logs package
> Message-ID:
>         <CAPvvxJX-cs7se4cicZ+BZyzPbAL02OmQq-z662e=ad74+uxNfQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> On Tue, Oct 7, 2014 at 4:51 PM, Duncan Murdoch <murdoch.duncan at gmail.com>
> 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 ?crit :
>>> > 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 Dar?czi a ?crit :
>>> >> > On Tue, Oct 7, 2014 at 2:21 PM, Duncan Murdoch
>>> >> > <murdoch.duncan at gmail.com> 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 at 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
>>> >>
>>>
>>>
>>



[Rd] [R logs] Help in develop a simply logs package
Thomas J. Leeper