Re: [Rd] should the text for RIGHT_ASSIGN be -> in getParseData()?
Here are two more standard emacs bindings that work: Ctrl-K to cut and Ctrl-Y
to paste.
•
Brian Lee Yung Rowe
917 496 4583
On Jul 5, 2013, at 2:32 PM, William Dunlap wrote:
>> But up-arrow, ctrl-A then "z <-" is not much less convenient, is it?
>
> I didn't know that ctrl-A would bring me to the start of the line, nor
> that ctrl-E would bring me to the end. Thanks.
>
> Bill Dunlap
> Spotfire, TIBCO Software
> wdunlap tibco.com
>
>
>> -Original Message-
>> From: peter dalgaard [mailto:pda...@gmail.com]
>> Sent: Friday, July 05, 2013 11:25 AM
>> To: William Dunlap
>> Cc: Barry Rowlingson; R-devel
>> Subject: Re: [Rd] should the text for RIGHT_ASSIGN be -> in getParseData()?
>>
>>
>> On Jul 5, 2013, at 18:59 , William Dunlap wrote:
>>
>>>> Is there any reason right-assign with "->" still exists? How much
>>>> code on CRAN uses it, and how trivially could it be excised?
>>>
>>> I use '->' a lot when doing interactive work. I often first run a command
>>> to see its printed output then decide that I had better save its value.
>>> The up-arrow key gives me the previous command line with the cursor placed
>>> at the
>>> end of the line so adding '-> z' at the end of the line is convenient.
>>> (Not using the up-arrow key and doing 'z <- .Last.value' also works, but
>>> I don't like its context sensitivity.)
>>
>> But up-arrow, ctrl-A then "z <-" is not much less convenient, is it?
>>
>> I have used in with multi-line input, occasionally, though. As in
>>
>> replicate(1, {
>> ysim <- rbinom(length(p), n, p)
>> glm(cbind(ysim, n - ysim) ~ x, binomial)$deviance
>> })
>>
>> ... and then you realize that you probably don't want to look at 1
>> simulated
>> deviances and add "-> simDev".
>>
>>>
>>> I never use '->' when writing code in a file, so you would have to search
>>> my .Rhistory files, not my *.R files, for evidence of its usefulness to me.
>>>
>>> Bill Dunlap
>>> Spotfire, TIBCO Software
>>> wdunlap tibco.com
>>>
>>>
>>>> -Original Message-
>>>> From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org]
>>>> On
>> Behalf
>>>> Of Barry Rowlingson
>>>> Sent: Friday, July 05, 2013 9:29 AM
>>>> To: Duncan Murdoch
>>>> Cc: R-devel
>>>> Subject: Re: [Rd] should the text for RIGHT_ASSIGN be -> in getParseData()?
>>>>
>>>> On Fri, Jul 5, 2013 at 12:57 PM, Duncan Murdoch
>>>> wrote:
>>>>
>>>>> R itself doesn't make use of the text column, it's for display of code
>>>>> by highlighters etc. So if anyone does assume text is a function name,
>>>>> it's their bug, not ours. In fact, the bug is already there, because
>>>>> there is actually one other example which was being parsed properly,
>>>>> "**" is translated to "^". There's no `**` function, but 2**3 works.
>>>>
>>>> Is there any reason right-assign with "->" still exists? How much
>>>> code on CRAN uses it, and how trivially could it be excised? Can we
>>>> also have 'up assign' and "down assign" so I can do:
>>>>
>>>>> 3
>>>>> x -^
>>>>> x -v
>>>>> 4
>>>>
>>>> - they make just as much sense.
>>>>
>>>> Okay, lets see all the edge cases.
>>>>
>>>> Barry
>>>>
>>>> __
>>>> 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
>>
>> --
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Email: pd@cbs.dk Priv: pda...@gmail.com
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel
__
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Re: [Rd] should the text for RIGHT_ASSIGN be -> in getParseData()?
That is a more accurate statement regarding Ctrl-K. Nonetheless whatever is
killed can be yanked back via Ctrl-Y, so the effect emulates cutting and
pasting. I am also a vi user, but these four basic emacs bindings seem to
perennially haunt numerous terminal apps.
•
Brian Lee Yung Rowe
917 496 4583
On Jul 5, 2013, at 3:53 PM, William Dunlap wrote:
> Ctrl-K is delete from here to end of line on Linux-comand-line and
> Windows-GUI R.
> (My fingers are not nimble enough for emacs, I'll stick with vi.)
>
> Bill Dunlap
> Spotfire, TIBCO Software
> wdunlap tibco.com
>
>
>> -----Original Message-
>> From: Brian Lee Yung Rowe [mailto:r...@muxspace.com]
>> Sent: Friday, July 05, 2013 12:11 PM
>> To: William Dunlap
>> Cc: peter dalgaard; R-devel; Barry Rowlingson
>> Subject: Re: [Rd] should the text for RIGHT_ASSIGN be -> in getParseData()?
>>
>> Here are two more standard emacs bindings that work: Ctrl-K to cut and
>> Ctrl-Y to paste.
>>
>> •
>> Brian Lee Yung Rowe
>> 917 496 4583
>>
>>
>> On Jul 5, 2013, at 2:32 PM, William Dunlap wrote:
>>
>>>> But up-arrow, ctrl-A then "z <-" is not much less convenient, is it?
>>>
>>> I didn't know that ctrl-A would bring me to the start of the line, nor
>>> that ctrl-E would bring me to the end. Thanks.
>>>
>>> Bill Dunlap
>>> Spotfire, TIBCO Software
>>> wdunlap tibco.com
>>>
>>>
>>>> -Original Message-
>>>> From: peter dalgaard [mailto:pda...@gmail.com]
>>>> Sent: Friday, July 05, 2013 11:25 AM
>>>> To: William Dunlap
>>>> Cc: Barry Rowlingson; R-devel
>>>> Subject: Re: [Rd] should the text for RIGHT_ASSIGN be -> in getParseData()?
>>>>
>>>>
>>>> On Jul 5, 2013, at 18:59 , William Dunlap wrote:
>>>>
>>>>>> Is there any reason right-assign with "->" still exists? How much
>>>>>> code on CRAN uses it, and how trivially could it be excised?
>>>>>
>>>>> I use '->' a lot when doing interactive work. I often first run a command
>>>>> to see its printed output then decide that I had better save its value.
>>>>> The up-arrow key gives me the previous command line with the cursor
>>>>> placed at the
>>>>> end of the line so adding '-> z' at the end of the line is convenient.
>>>>> (Not using the up-arrow key and doing 'z <- .Last.value' also works, but
>>>>> I don't like its context sensitivity.)
>>>>
>>>> But up-arrow, ctrl-A then "z <-" is not much less convenient, is it?
>>>>
>>>> I have used in with multi-line input, occasionally, though. As in
>>>>
>>>> replicate(1, {
>>>> ysim <- rbinom(length(p), n, p)
>>>> glm(cbind(ysim, n - ysim) ~ x, binomial)$deviance
>>>> })
>>>>
>>>> ... and then you realize that you probably don't want to look at 1
>>>> simulated
>>>> deviances and add "-> simDev".
>>>>
>>>>>
>>>>> I never use '->' when writing code in a file, so you would have to search
>>>>> my .Rhistory files, not my *.R files, for evidence of its usefulness to
>>>>> me.
>>>>>
>>>>> Bill Dunlap
>>>>> Spotfire, TIBCO Software
>>>>> wdunlap tibco.com
>>>>>
>>>>>
>>>>>> -Original Message-
>>>>>> From: r-devel-boun...@r-project.org
>>>>>> [mailto:r-devel-boun...@r-project.org] On
>>>> Behalf
>>>>>> Of Barry Rowlingson
>>>>>> Sent: Friday, July 05, 2013 9:29 AM
>>>>>> To: Duncan Murdoch
>>>>>> Cc: R-devel
>>>>>> Subject: Re: [Rd] should the text for RIGHT_ASSIGN be -> in
>>>>>> getParseData()?
>>>>>>
>>>>>> On Fri, Jul 5, 2013 at 12:57 PM, Duncan Murdoch
>>>>>> wrote:
>>>>>>
>>>>>>> R itself doesn't make use of the text column, it's for display of code
>>>>>>> by highlighters etc. So if anyone does assume text is a function name,
>>>>>>> it's their bug, not ours. In fact, the bug is already there, because
>>>>>>> there is a
Re: [Rd] legitimate use of :::
You raise an interesting point that I've mulled over a bit: namespace collisions. How many of these issues would go away if there were a better mechanism for managing namespaces? eg in other languages you can control which objects/modules you wish to import from a library. Under this regime I think package developers would be less concerned about exposing functions that otherwise would be private. On Aug 22, 2013, at 6:27 PM, Gabor Grothendieck wrote: > If ::: is disallowed then its likely that package developers will need > to export more functions to satisfy the consumers of those otherwise > hidden functions but if more functions are exported then there > will be a greater likelihood of conflicts among packages. > > The problem seems to be that there are potentially three sorts of > functions here: > > 1. a function is hidden > 2. a function is accessible via ::: but is not on the search path > 3. a function is on the search path > > The problem arises in attempting to force fit these three concepts > into only two > categories either by removing the first category (as was done previously) > or by removing the second category (which seems to be the new approach). __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] legitimate use of :::
This is what I was getting at as well. It would be great to have a call like
require(package, c('funtion.1','function.2'))
or similar that gives users granular control over what gets imported in the
shell. I would be drunk with joy if the same mechanism could be used to
automatically populate the package directives.
On Aug 22, 2013, at 8:01 PM, Peter Meilstrup wrote:
> It would be nice if the functionality of importFrom() and import() were
> available to user level code, rather than just to people building packages
> for distribution. One most often encounters namespace conflicts at the user
> level, when loading two packages that have no logical connection other than
> both bearing on your problem of the moment.
>
> R conflates "having namespaces" with "having a library distribution
> mechanism" and while its library distribution mechanism is top notch, most
> modern languages do not require you to learn the distribution procedure in
> order to just have namespaces.
>
> For instance, in Python you merely put code in a file called foo.py and
> then in any other file in the same directory you type "import functionName
> from foo". I.E. using namespaces does not require you to build/install
> packages. Python namespaces are also hierarchical so that the question of
> this thread would easily be resolved by putting functions into
> foo._internal and in other packages typing import * from "foo._internal"
>
> Peter
>
> [[alternative HTML version deleted]]
>
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Re: [Rd] R CMD config for R >= 3.0.1
As an alternative, you might consider installing a virtual machine in your user space and installing R from there. That way you don't have to do a bunch of one-off gymnastics to get R compiled. On Sep 11, 2013, at 1:40 AM, Simon Urbanek wrote: > On Sep 10, 2013, at 5:30 PM, crunch wrote: > >> Also have no cooperation from the admin of the machine, so can't ask for a >> yum install. > > Please follow Brian's advice. If you don't have even Fortran on that machine, > then you're really in a pickle: you can extract the gfortran rpm contents > (and all dependencies you may need) by hand in any place that you have access > to and adjust LD_LIBRARY_PATH for the runtime accordingly. However, it's not > a trivial task - it particular if you're not very familiar with subtleties of > Linux. (I had to do this fairly recently on a CentOS machine, so I know it's > possible, but there are a few gotchas that may require a few symlinks created > by hand). > > Cheers, > Simon > > >> >> -- >> View this message in context: >> http://r.789695.n4.nabble.com/R-CMD-config-for-R-3-0-1-tp4667399p4675814.html >> Sent from the R devel mailing list archive at Nabble.com. >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] declaring package dependencies
I haven't used rforge, but I will look check out the scripts. The reason it would be a six-pack of work is that there are generic build systems that handle most of this work. What they don't do is act as a repository, so rforge could remain that while separating out the build process. On Sep 16, 2013, at 4:58 AM, Matthew Dowle wrote: > On Sep 16, 2013, at 01:46 PM, Brian Rowe wrote: > >> That reminds me: I once made a suggestion on how to automate some of the CRAN >> deployment process, but it was shot down as not being useful to them. I do >> recall a quote that was along the lines of "as long as you don't need help, >> do whatever you want", so one thought is to just set up a build server that >> does the building across the three versions of R, checks dependencies, >> rebuilds >> when release, patch, or devel are updated, etc. This would ease the burden on >> package maintainers and would just happen to make the CRAN folks' lives >> easier >> by catching a lot of bad builds. A proof of concept on AWS connecting to >> github >> or rforge could probably be finished on a six-pack. Speak up if anyone thinks >> this would be useful. > > Yes useful. But that includes a package build system (which is what breaks on > R-Forge). If you could do that on a six-pack then could you fix R-Forge on a > three-pack first please? The R-Forge build system is itself an open source > package on R-Forge. Anyone can look at it, understand it and change it to be > more stable. That build system is here : > > https://r-forge.r-project.org/R/?group_id=34 > > (I only know this because Stefan told me once. So I suspect others don't know > either, or it hasn't sunk in that we're pushing on an open door.) > > Matthew > > __ > 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] Where to drop a python script?
If that's all you want to do, you can ignore the headache by just calling
system("python -V").
Then you don't need to save any python scripts.
On Nov 1, 2013, at 10:17 AM, Jonathan Greenberg wrote:
> This was actually the little script I was going to include (prompting me to
> ask the question): a test for the python version number.
> Save this (between the ***s) as e.g. python_version.py:
>
> ***
>
> import sys
> print(sys.version_info)
>
> ***
>
> I've done almost no python coding, so I was going to call this with a
> system("/pathto/python /pathto/python_version.py",intern=TRUE) call and
> post-process the one-line text output.
>
> --j
>
>
> On Thu, Oct 31, 2013 at 12:45 PM, Paul Gilbert wrote:
>
>>
>>
>> On 13-10-31 01:16 PM, Prof Brian Ripley wrote:
>>
>>> On 31/10/2013 15:33, Paul Gilbert wrote:
>>>
On 13-10-31 03:01 AM, Prof Brian Ripley wrote:
> On 31/10/2013 00:40, Paul Gilbert wrote:
>
>> The old convention was that it went in the exec/ directory, but as you
>> can see at
>> http://cran.at.r-project.org/**doc/manuals/r-devel/R-exts.**
>> html#Non_002dR-scripts-in-**packages
>>
>>
>>
>> it can be in inst/anyName/. A minor convenience of exec/ is that the
>> directory has the same name in source and when installed, whereas
>> inst/anyName gets moved to anyName/, so debugging can be a tiny bit
>> easier with exec/.
>>
>> Having just put a package (TSjson) on CRAN with a python script, here
>> are a few other pointers for getting it on CRAN:
>>
>> -SystemRequirements: should indicate if a particular version of python
>> is needed, and any non-default modules that are needed. (My package
>> does
>> not work with Python 3 because some modules are not available.) Some of
>> the libraries have changed, so it could be a bit tricky to make
>> something work easily with both 2 and 3.
>>
>> -You need a README to explain how to install Python. (If you look at or
>> use mine, please let me know if you find problems.)
>>
>
> Better to describe exactly what you need: installation instructions go
> stale very easily.
>
> -The Linux and Sun CRAN test machines have Python 2 whereas winbuilder
>> has Python 3. Be prepared to explain that the package will not work on
>> one or the other.
>>
>
> Not true. Linux and Solaris (sic) have both: the Solaris machines have
> 2.6 and 3.3.
>
For an R package how does one go about specifying which should be used?
>>>
>>> You ask the user to tell you the path or at least the command name, e.g.
>>> by an environment variable or R function argument. Just like any other
>>> external program such as GhostScript.
>>>
>>
>> Yes, but since I don't have direct access to the CRAN test machines,
>> specifically, on the CRAN test machines, how do I specify to use Python 2
>> or Python 3? (That is, I think you are the user when CRAN tests are done on
>> Solaris, so I am asking you.)
>>
>>
>>
>>>
Please do not spread misinformation about machines you do
> not have any access to.
>
>
>> Another option to system() is pipe()
>>
>> Paul
>>
>> On 13-10-30 03:15 PM, Dirk Eddelbuettel wrote:
>>
>>>
>>> On 30 October 2013 at 13:54, Jonathan Greenberg wrote:
>>> | R-developers:
>>> |
>>> | I have a small python script that I'd like to include in an R
>>> package I'm
>>> | developing, but I'm a bit unclear about which subfolder it should go
>>> in. R
>>> | will be calling the script via a system() call. Thanks!
>>>
>>> Up to you as you control the path. As "Writing R Extensions" explains,
>>> everything below the (source) directory inst/ will get installed. I
>>> like
>>> inst/extScripts/ (or similar) as it denotes that it is an external
>>> script.
>>>
>>> As an example, the gdata package has Perl code for xls reading/writing
>>> below a
>>> directory inst/perl/ -- and I think there are more packages doing
>>> this.
>>>
>>> Dirk
>>>
>>>
>>>
>> __**
>> 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
>>
>
>
>
> --
> Jonathan A. Greenberg, PhD
> Assistant Professor
> Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
> Department of Geography and Geographic Information Science
> University of Illinois at Urbana-Champaign
> 259 Computing Applicati
[Rd] Behavior of --install-tests and testInstalledPackage
Hello, I'm writing a script that automates the testing of reverse dependencies of a package. I found the function testInstalledPackage in the tools package, which seems to do what I want. However, when I use it for a source package that was installed with --install-tests, I've noticed that only the actual test files (e.g. located in inst/tests) are available and run. In other words the test harness script (e.g. in tests) is not copied, so any wiring to run tests isn't available when running testInstalledPackage. I tried loading the required packages (i.e. the installed package to retest plus the testing frameworks RUnit, testthat), but since testInstalledPackage makes an external call to R CMD BATCH, any packages loaded in my current environment have no effect on the tests. The only workaround that I've come up with is to add require statements to the top of each test file, but this is a bit onerous. My question is whether 1) there is a technique to force the test harness script (e.g. tests/run_tests.R, tests/doRUnit.R) to be copied into the installed source package, or 2) there is a way to have testInstalledPackage force the loading of required packages prior to executing test scripts, or 3) has someone already done this? Thanks and Regards, Brian __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Behavior of --install-tests and testInstalledPackage
Winston,
Thanks for the pointer. Hadley made the same suggestion. One thing I was
looking to do though was have something like this automated, so it would be
nice to have a return value instead of just results written to files. That's
one nice thing about the testInstalledPackage function, despite the issue with
the test harness. Any additional pointers are greatly appreciated.
Warm Regards,
Brian Rowe
â¢â¢â¢â¢â¢
Brian Lee Yung Rowe
Founder, Zato Novo
Professor
On Jan 27, 2014, at 12:52 PM, Winston Chang wrote:
> On Wed, Jan 22, 2014 at 10:55 AM, Brian Lee Yung Rowe
> wrote:
>> Hello,
>>
>> I'm writing a script that automates the testing of reverse dependencies of a
>> package. I found the function testInstalledPackage in the tools package,
>> which seems to do what I want. However, when I use it for a source package
>> that was installed with --install-tests, I've noticed that only the actual
>> test files (e.g. located in inst/tests) are available and run. In other
>> words the test harness script (e.g. in tests) is not copied, so any wiring
>> to run tests isn't available when running testInstalledPackage.
>>
>> I tried loading the required packages (i.e. the installed package to retest
>> plus the testing frameworks RUnit, testthat), but since testInstalledPackage
>> makes an external call to R CMD BATCH, any packages loaded in my current
>> environment have no effect on the tests. The only workaround that I've come
>> up with is to add require statements to the top of each test file, but this
>> is a bit onerous.
>>
>> My question is whether
>> 1) there is a technique to force the test harness script (e.g.
>> tests/run_tests.R, tests/doRUnit.R) to be copied into the installed source
>> package, or
>> 2) there is a way to have testInstalledPackage force the loading of required
>> packages prior to executing test scripts, or
>> 3) has someone already done this?
>
>
> I can answer (3). devtools already has a function that does this:
> library(devtools)
> revdep_check('mypackage')
>
> It's basically a wrapper for the revdep and check_cran functions from
> devtools. In the development version of devtools (on Github) there are some
> changes to improve the output of these functions.
>
> -Winston
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Re: [Rd] Ellipsis to Two Functions When One Has Nested Functions
Another option is to use a closure, which isolates the arguments explicitly.
aFunction <- function(data, alpha, ...)
{
transform(alpha, ...)
rowMeans(data) > alpha
}
f <- function(data, selection, ...)
{
selected <- selection(data) # Remove ellipsis from here
plot(data[selected, ], ...)
}
f(aDataset, function(data) aFunction(data, alpha = 10, transform = sqrt), pch =
19)
Brian Lee Yung Rowe
Founder, Zato Novo
Professor, M.S. Data Analytics, CUNY
On May 28, 2014, at 7:34 AM, Duncan Murdoch wrote:
> On 28/05/2014, 2:00 AM, Dario Strbenac wrote:
>> Hello
>>
>> If I have a function
>>
>> aFunction <- function(data, alpha, ...)
>> {
>> transform(alpha, ...)
>> rowMeans(data) > alpha
>> }
>>
>> f <- function(data, selection, ...)
>> {
>> selected <- selection(data, ...)
>> plot(data[selected, ], ...)
>> }
>>
>> f(aDataset, aFunction, alpha = 10, pch = 19, transform = sqrt)
>>
>> and selection calls another function, which has ... and that function calls
>> other functions, is there an easier way than getting the formals of all the
>> functions called internally by selection, and all of the formals of
>> functions called by plot ? Is there any option to change the error into a
>> warning message ?
>
> You can use try() to catch an error, but you can't ignore it. The code that
> triggered the error will still exit at that point.
>
> There are at least two common ways of handling the situation where you want
> to pass optional args to two different functions. One is to use
>
> args <- list(...)
>
> to get all the arguments in a list, and then manually split up the list, and
> use do.call() to pass some of them on. Generally you would do this only if
> you knew in advance how to split the args, you wouldn't try to call formals()
> to work it out at run-time.
>
> Another way is to have an argument like "control" in optim(), and ask the
> user to pass one set of options via that, and the other via ... . You'd use
> do.call() again to construct that call.
>
> Duncan Murdoch
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel
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Re: [Rd] Ellipsis to Two Functions When One Has Nested Functions
Another option is to use a closure, which isolates the arguments explicitly.
aFunction <- function(data, alpha, ...)
{
transform(alpha, ...)
rowMeans(data) > alpha
}
f <- function(data, selection, ...)
{
selected <- selection(data) # Remove ellipsis from here
plot(data[selected, ], ...)
}
f(aDataset, function(data) aFunction(data, alpha = 10, transform = sqrt), pch =
19)
Brian Lee Yung Rowe
Founder, Zato Novo
Professor, M.S. Data Analytics, CUNY
On May 28, 2014, at 7:34 AM, Duncan Murdoch wrote:
> On 28/05/2014, 2:00 AM, Dario Strbenac wrote:
>> Hello
>>
>> If I have a function
>>
>> aFunction <- function(data, alpha, ...)
>> {
>> transform(alpha, ...)
>> rowMeans(data) > alpha
>> }
>>
>> f <- function(data, selection, ...)
>> {
>> selected <- selection(data, ...)
>> plot(data[selected, ], ...)
>> }
>>
>> f(aDataset, aFunction, alpha = 10, pch = 19, transform = sqrt)
>>
>> and selection calls another function, which has ... and that function calls
>> other functions, is there an easier way than getting the formals of all the
>> functions called internally by selection, and all of the formals of
>> functions called by plot ? Is there any option to change the error into a
>> warning message ?
>
> You can use try() to catch an error, but you can't ignore it. The code that
> triggered the error will still exit at that point.
>
> There are at least two common ways of handling the situation where you want
> to pass optional args to two different functions. One is to use
>
> args <- list(...)
>
> to get all the arguments in a list, and then manually split up the list, and
> use do.call() to pass some of them on. Generally you would do this only if
> you knew in advance how to split the args, you wouldn't try to call formals()
> to work it out at run-time.
>
> Another way is to have an argument like "control" in optim(), and ask the
> user to pass one set of options via that, and the other via ... . You'd use
> do.call() again to construct that call.
>
> Duncan Murdoch
>
> __
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Re: [Rd] index.search
Adrian,
You might consider using a unit testing framework such as RUnit or testthat,
which does this but in a more structured manner. Essentially you codify the
behavior in a set of tests as opposed to comparing with a previous version.
HTH,
Brian
â¢â¢â¢â¢â¢
Brian Lee Yung Rowe
Founder, Zato Novo
Professor, M.S. Data Analytics, CUNY
> On Jun 15, 2014, at 11:25 PM, "Adrian DuÈa" wrote:
>
> Hi Gabriel,
>
> Actually, I am not going to use multiple versions of the same package,
> but always the last version. What I would like to do is:
> - to run all examples from all functions in the package, saving the
> results into a list
> - compare the list to an already saved one (from the previous version
> of the package), possibly using all.equal()
>
> I tried using the example() function, like this:
> example("deMorgan", package="QCA", give.lines=TRUE)
>
> That returns the commands from the examples section, but if a command
> is split over multiple rows I cannot use it automatically.
>
> I could also use:
> capture.output(example("deMorgan", package="QCA", ask=FALSE))
>
> That would indeed work for the printed output, but I would also like
> to compare the objects saved by the deMorgan() function. If that is
> not possible, I'll probably be happy with the printed output.
>
> I'd still be curious as to why the index.search() function cannot be
> used... (it seems useful for other purposes).
>
> Best wishes,
> Adrian
>
>
>> On Mon, Jun 16, 2014 at 5:46 AM, Gabriel Becker wrote:
>> Adrian,
>>
>> R isn't really designed to use multiple versions of the same package in the
>> same R session. To do what you want you'll need to unload one version of the
>> package before you load the next, which will work some percentage of the
>> time between 50 and 100 ("usually"), but when it can be done it is
>> relatively easy to do.
>>
>> Packages with C code will give you problems, or at least they used to. I
>> haven't tried recently. See Prof Ripley's response here: See
>> https://stat.ethz.ch/pipermail/r-devel/2009-February/052229.html
>>
>> For packages that can be unloaded/reloaded safely, is there a reason you
>> can't just use the existing example function with two different library
>> locations (lib.loc argument) with the two package versions installed?
>>
>> ~G
>>
>>
>>> On Sun, Jun 15, 2014 at 6:22 PM, Adrian DuÈa wrote:
>>>
>>> Dear r-devel,
>>>
>>> I am trying to automatically check if two successive versions of a
>>> package have the same results (i.e. code not broken), by parsing the
>>> example sections for each function against a previously tested
>>> version.
>>>
>>> While trying to replicate the code from example(), I am facing an
>>> error related with te "index.search" function (line 7 in the example()
>>> code).
>>> This is the code I am using:
>>>
>>> example2 <- function (topic, package = NULL, lib.loc = NULL,
>>> character.only = FALSE,
>>>give.lines = FALSE, local = FALSE, echo = TRUE, verbose =
>>> getOption("verbose"),
>>>setRNG = FALSE, ask = getOption("example.ask"), prompt.prefix =
>>> abbreviate(topic, 6), run.dontrun = FALSE)
>>> {
>>>if (!character.only) {
>>>topic <- substitute(topic)
>>>if (!is.character(topic))
>>>topic <- deparse(topic)[1L]
>>>}
>>>pkgpaths <- find.package(package, lib.loc, verbose = verbose)
>>>file <- index.search(topic, pkgpaths, TRUE)
>>>return(file)
>>> }
>>>
>>>> example2("deMorgan", package="QCA")
>>> Error in example2("deMorgan", package = "QCA") :
>>> could not find function "index.search"
>>>
>>>
>>> I've tried an explicit library(utils), with the same result.
>>> ?index.search doesn't yield anything better...
>>>
>>> Could anyone point me in the right direction, please?
>>> Thank you,
>>> Adrian
>>>
>>>
>>> --
>>> Adrian Dusa
>>> University of Bucharest
>>> Romanian Social Data Archive
>>> 1, Schitu Magureanu Bd.
>>> 050025 Bucharest sector 5
>>> Romania
>>> Tel.:+40 21 3126618 \
>>>+40 21 3120210 / int.101
>>> Fax: +40 21 3158391
>>>
>>> __
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>>
>>
>> --
>> Gabriel Becker
>> Graduate Student
>> Statistics Department
>> University of California, Davis
>
>
>
> --
> Adrian Dusa
> University of Bucharest
> Romanian Social Data Archive
> 1, Schitu Magureanu Bd.
> 050025 Bucharest sector 5
> Romania
> Tel.:+40 21 3126618 \
>+40 21 3120210 / int.101
> Fax: +40 21 3158391
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel
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Re: [Rd] index.search
Thanks for the great insight. I love that there's always something else to
learn in R.
â¢â¢â¢â¢â¢
Brian Lee Yung Rowe
Founder, Zato Novo
Professor, M.S. Data Analytics, CUNY
On Jun 16, 2014, at 3:34 AM, Martin Maechler wrote:
>>>>>> Adrian DuÈa
>>>>>>on Mon, 16 Jun 2014 08:33:59 +0300 writes:
>
>> On Mon, Jun 16, 2014 at 6:37 AM, Gabriel Becker
>> wrote:
>>> [...] You can. This is valid R source, so the parser
>>> will understand it
>>>
>>> expr = parse(text= example("deMorgan", package="QCA",
>>> give.lines=TRUE))
>>>
>>> You can then evaluate some or all of that expression
>>> using either R's own eval package or, e.g. Hadley
>>> Wickham's evaluate package (for your particular usecase
>>> evaluate will be easier I think).
>
>> Oh, I see...! In that case I can use it, of course. Did
>> install the evaluate package, although one would expect
>> some better documentation (no examples at all, especially
>> at the main evaluate function).
>
>
>>>> [...]
>>> index.search is an unexported function, which means that
>>> it is subject to change in how it behaves without notice
>>> or even externally available reasons. You can get it via
>>> :::, but again, it's really not the right tool here, and
>>> not safe to use in general in code you expect to keep
>>> working.
>
>> Yes, I figured that much. Of course it's not meant to be
>> used in any decently working code, but I learn heavily by
>> simply looking at these sort of (hidden) R functions.
>
>> Thanks again, Adrian
>
> Apropos "not the right tool". I'm a bit astonished that nobody
> mentioned the fact R already provides "the tool" to
> automatically compare all example outputs with a previous
> version (of the packages example outputs):
>
> *THE* manual (every package writer should know about,
> re-read/browse about once a year, and search in for such questions):
>
> "Writing R Extensions", section Package subdirectories
>
> (e.g. on the CRAN master in Vienna,
> http://cran.r-project.org/doc/manuals/R-exts.html#Package-subdirectories )
> says
>
> |If directory 'tests' has a subdirectory 'Examples' containing a file
> |'PKG-Ex.Rout.save', this is compared to the output file for running the
> |examples when the latter are checked.
>
> So: After an 'R CMD check ' you only need to take and
> keep the -Ex.Rout file that is produced (in the
> PKG.Rcheck/ directory), and save it into /tests/-Ex.Rout.save
> and from then on, every time you run R CMD check the
> comparison will be made.
>
> Martin Maechler, ETH Zurich
>
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Re: [Rd] modifying a persistent (reference) class
Ross, This is generally a hard problem in software systems. The only language I know that explicitly addresses it is Erlang. Ultimately you need a system upgrade process, which defines how to update the data in your system to match a new version of the system. You could do this by writing a script that 1) loads the old version of your library 2) loads your data/serialized reference classes 3) exports data to some intermediate format (eg a list) 4) loads new version of library 5) imports data from intermediate format Once you've gone through the upgrade process, arguably it's better to persist the data in a format that is decoupled from your objects since then future upgrades would simply be 1) load new library 2) import data from intermediate format which is no different from day-to-day operation of your app/system (ie you're always writing to and reading from the intermediate format). Warm regards, Brian â¢â¢â¢â¢â¢ Brian Lee Yung Rowe Founder, Zato Novo Professor, M.S. Data Analytics, CUNY > On Aug 1, 2014, at 1:54 PM, Ross Boylan wrote: > > I saved objects that were defined using several reference classes. > Later I modified the definition of reference classes a bit, creating new > functions and deleting old ones. The total number of functions did not > change. When I read them back I could only access some of the original > data. > > I asked on the user list and someone suggested sticking with the old > class definitions, creating new classes, reading in the old data, and > converting it to the new classes. This would be awkward (I want the > "new" classes to have the same name as the "old" ones), and I can > probably just leave the old definitions and define the new functions I > need outside of the reference classes. > > Are there any better alternatives? > > On reflection, it's a little surprising that changing the code for a > reference class makes any difference to an existing instance, since all > the function definitions seem to be attached to the instance. One > problem I've had in the past was precisely that redefining a method in a > reference class did not change the behavior of existing instances. So > I've tried to follow the advice to keep the methods light-weight. > > In this case I was trying to move from a show method (that just printed) > to a summary method that returned a summary object. So I wanted to add > a summary method and redefine the show to call summary in the base > class, removing all the subclass definitions of show. > > Regular S4 classes are obviously not as sensitive since they usually > don't include the functions that operate on them, but I suppose if you > changed the slots you'd be in similar trouble. > > Some systems keep track of versions of class definitions and allow one > to write code to migrate old to new forms automatically when the data > are read in. Does R have anything like that? > > The system on which I encountered the problems was running R 2.15. > > __ > 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] modifying a persistent (reference) class
Ross, Ah I didn't think about Smalltalk. Doesn't surprise me that they supported upgrades of this sort. That aside I think the question is whether it's realistic for a language like R to support such a mechanism automatically. Smalltalk and Erlang both have tight semantics that would be hard to establish in R (given the multiple object systems and dispatching systems). I'm a functional guy so to me it's natural to separate the data from the functions/methods. Having spent years writing OOP code I walked away concluding that OOP makes things more complicated for the sake of being OOP (eg no first class functions). Obviously that's changing, and in a language like R it's less of an issue. However, something like object serialization smells suspiciously similar. If you know that serializing objects is brittle, why not look for an alternative approach as opposed to chasing that rainbow? Warm regards, Brian â¢â¢â¢â¢â¢ Brian Lee Yung Rowe Founder, Zato Novo Professor, M.S. Data Analytics, CUNY > On Aug 1, 2014, at 3:33 PM, Ross Boylan wrote: > >> On Fri, 2014-08-01 at 14:42 -0400, Brian Lee Yung Rowe wrote: >> Ross, >> >> >> This is generally a hard problem in software systems. The only >> language I know that explicitly addresses it is Erlang. Ultimately you >> need a system upgrade process, which defines how to update the data in >> your system to match a new version of the system. You could do this by >> writing a script that >> 1) loads the old version of your library >> 2) loads your data/serialized reference classes >> 3) exports data to some intermediate format (eg a list) >> 4) loads new version of library >> 5) imports data from intermediate format > My recollection is that in Gemstone's smalltalk database you can define > methods associated with a class that describe how to change an instance > from one version to another. You also have the choice of upgrading all > persistent objects at once or doing so lazily, i.e., as they are > retrieved. > > The brittleness of the representation depends partly on the details. If > a class has 2 slots, a and b, and the only thing on disk is the contents > of a and the contents of b, almost any change will screw things up. > However, if the slot name is persisted with the instance it's much > easier to reconstruct the instance of the class changes (if slot c is > added and not on disk, set it to nil; if b is removed, throw it out when > reading from disk). Once could also persist the class definition, or > key elements of it, with individual instances referring to the > definition. > > I don't know which, if any of these strategies, R uses for reference or > other classes. >> >> >> Once you've gone through the upgrade process, arguably it's better to >> persist the data in a format that is decoupled from your objects since >> then future upgrades would simply be >> 1) load new library >> 2) import data from intermediate format > Arguably :) As I said, some representations could do this > automatically. And there are still issues such as a change in the type > of a slot, or rules for filling new slots, that would require > intervention. > > In my experience with other object systems, usually methods are > attributes of the class. For R reference classes they appear to be > attributes of the instance, potentially modifiable on a per-instance > basis. > > Ross >> >> >> which is no different from day-to-day operation of your app/system (ie >> you're always writing to and reading from the intermediate format). >> >> >> Warm regards, >> Brian >> >> â¢â¢â¢â¢â¢ >> Brian Lee Yung Rowe >> Founder, Zato Novo >> Professor, M.S. Data Analytics, CUNY >> >> On Aug 1, 2014, at 1:54 PM, Ross Boylan wrote: >> >> >>> I saved objects that were defined using several reference classes. >>> Later I modified the definition of reference classes a bit, creating >>> new >>> functions and deleting old ones. The total number of functions did >>> not >>> change. When I read them back I could only access some of the >>> original >>> data. >>> >>> I asked on the user list and someone suggested sticking with the old >>> class definitions, creating new classes, reading in the old data, >>> and >>> converting it to the new classes. This would be awkward (I want the >>> "new" classes to have the same name as the "old" ones), and I can >>> probably just leave the old definitions and define the new functions &
Re: [Rd] Compilation problems
I would add it would be useful to know what system you are on and how much
overall memory the machine has (not to mention how many other users are on the
box). If you are on a linux variant, you can see installed memory by running:
cat /proc/meminfo. You might also want to look at top to see how many resources
are being used by you and others.
Regarding Java, if you had done a search for 'java xmx', you'd see that you can
control the maximum heap size of the JVM using this option. [1] So, if you
know how much memory you have available on your system, then you can set this
value to something lower and verify that you can start the JVM in isolation. As
for specifics, I wouldn't know, since you didn't provide the JVM version you're
using. Try java -version to give us specifics.
Brian
[1]
http://docs.oracle.com/cd/E13150_01/jrockit_jvm/jrockit/jrdocs/refman/optionX.html
�
Brian Lee Yung Rowe
Founder, Zato Novo
Professor, M.S. Data Analytics, CUNY
On Aug 13, 2014, at 5:15 AM, peter dalgaard wrote:
> Well, I didn't go there because I don't have a clue
>
> What I usually try in such circumstances is to Google the error message and
> see if any ideas crop up. Looks like it is common to several applications
> that use Java, so not likely an R issue per se.
>
> I'd look into
>
> - how to provoke the error to occur without make
> - what are your resource limits (ulimit -a is your friend)?
> - are any environment variables affecting the Java memory use? If not,
> perhaps you need to set them to values less than the max allowed. Or twiddle
> command line options.
>
> etc.
>
> -pd
>
> On 13 Aug 2014, at 10:46 , Andr� Z. D. A. wrote:
>
>> Thanks a lot for this atention, Peter. But the fonts problem is just a
>> warning: "configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF
>> vignettes and package manuals will not be rendered optimally". So, no
>> worries. I can live with render errors for the manuals. :)
>>
>> But the error I have with the 'make' is with Java. I don't know why. I even
>> restarted the compilation again (the only detail I change is to pass
>> "--prefix=/home/me/r/" to configure, to install it on my own folder instead
>> of defaults). Then a "make" without arguments and it ends with this:
>>
>> -
>> configuring Java ...
>> Java interpreter : /usr/bin/java
>> Could not create the Java virtual machine.
>> Error occurred during initialization of VM
>> Could not reserve enough space for object heap
>>
>> *** Java interpreter doesn't work properly.
>>
>> make[1]: [stamp-java] Error 1 (ignored)
>> make[1]: Leaving directory `/home/me/r-src-second-try/R-3.1.1'
>>
>> -
>>
>>
>> But how do anyone explain that onde a second run of 'make' it finished!? And
>> on two more times it won't show the error again!
>>
>> Lets try to run R. Done 'make install'... and then run... it works!
>>
>> I'm lost. A bug? Something is not working as it should? What? Or is it fine??
>>
>> Andre'
>>
>>
>>> On 11 Aug 2014, at 16:49 , peter dalgaard wrote:
>>>
>>>> On 11 Aug 2014, at 15:46 , Andr� Z. D. A. wrote:
>>>>
>>>>> No, Peter, I have the "(2014-07-10, Sock it to Me) R-3.1.1.tar.gz"
>>>>> source. Thanks for pointing it. So (I hope) it should be ok. Right?
>>>>
>>>> Not unlikely. (I goofed and thought that it only affected the development
>>>> version.)
>>>>
>>>> Check
>>>>
>>>> kpsewhich inconsolata.sty
>>>>
>>>> if it is found, and zi4.sty is not, then it should be fixed by an upcoming
>>>> patch release.
>>>
>>> ... and for a quick fix, edit the configure script. There is a section
>>> looking like this
>>>
>>> if test -n "${KPSEWHICH}"; then
>>> ${KPSEWHICH} zi4.sty > /dev/null
>>> if test $? -eq 0; then
>>> { $as_echo "$as_me:${as_lineno-$LINENO}: result: found zi4.sty" >&5
>>> $as_echo "found zi4.sty" >&6; }
>>> else
>>> ${KPSEWHICH} inconsolata.sty > /dev/null
>>> if test $? -ne 0; then
>>> { $as_echo "$as_me:${as_lineno-$LINENO}: result: found inconsolata.sty" >&5
>>>
>>> (Search for "incons" and you'll get ther
Re: [Rd] Is using devtools::release no longer allowed?
Isn't the source for CRAN itself open source? One option is to run a test
server that can respond with a success or failure message based on the
submission.
•
Brian Lee Yung Rowe
Founder, Zato Novo
Professor, M.S. Data Analytics, CUNY
> On Aug 19, 2014, at 3:55 PM, Kasper Daniel Hansen
> wrote:
>
> Given the seeming need for automated submission to CRAN, perhaps the repos
> maintainers could consider making a function available that allows one to
> do so, for example
> source("http://www.cran.r-project.org/submit_to_cran.R";)
> submit_to_cran("PACKAGE.TARBALL", REQUIRED_ARGUMENTS)
> or perhaps be interested in a community developed script? Although I
> recognize how easy it is for me to suggest work for others, it seems like
> such a script would cut down on everyones work, long-term.
>
> Best,
> Kasper
>
>
>
>
> On Tue, Aug 19, 2014 at 2:53 PM, Duncan Murdoch
> wrote:
>
>>> On 19/08/2014 2:40 PM, Carl Boettiger wrote:
>>>
>>> Dirk, listeners,
>>>
>>> Perhaps you would consider using omegahat's RHTMLForms instead?
>>>
>>> library("RHTMLForms")
>>> forms <- getHTMLFormDescription("http://xmpalantir.wu.ac.at/
>>> cransubmit/
>>> ")
>>> submit_to_cran <- createFunction(forms[[1]])
>>>
>>> Should create a function called "submit_to_cran" with arguments
>>> corresponding to the webform blanks, e.g.
>>>
>>> submit_to_cran(name = "packagename", email = "youremail", uploaded_file =
>>> "package.tar.gz", comment = "the optional comment")
>>>
>>> (clearly you could fill those details in from the submitting package
>>> description). I haven't tested this.
>> If you use this, make sure you test it well enough to get it perfect the
>> very first time you use it. If I were a CRAN administrator and received a
>> series of bad submissions from someone who was working out the bugs, I
>> would not find it difficult either technically or morally to permanently
>> ban that user from ever submitting anything again.
>>
>> Duncan Murdoch
>>
>>
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Re: [Rd] Why R-project source code is not on Github
One thing to note about git vs svn is that each git repository is a complete repository containing the full history, so despite github acting as a central repository, it is not the same as a central svn repository. In svn the central repository is typically the only repository with a complete revision history, but that is not the case with git. � Brian Lee Yung Rowe Founder, Zato Novo Professor, M.S. Data Analytics, CUNY On Aug 24, 2014, at 2:22 PM, Spencer Graves wrote: >> In addition, several members are skeptical about putting source code >> in the hands of a for-profit US company, and other legal issues. These >> are just some of the concerns that would need to be addressed to get >> everyone on board. > > > Am I correct that we could use Git without Github? > > > If yes, the planning might involve a cost-benefit comparison of what > would be required bring up a not-for-profit alternative to Github (e.g., > RGit.org or FreeGit.org or ...), and whether the risks of problems with that > would be more or less than the risks associated with "putting source code in > the hands of a for-profit US company". > > > Spencer > > > p.s. Regarding the risks of "putting source code in the hands of a > for-profit US company," I would naively expect that it should be easy and > cheap for someone to program a server to make daily backup copies of whatever > we want from Github. This could provide an insurance policy in case events > push the group to leave Github. Many (most?) of those who read this may > remember how LibreOffice forked from Open Office. A friend told me that > MySQL has a much larger user (and developer?) base than LibreOffice, and > every Oracle executive doubtless knows that MySQL could similarly be forked > relatively easily. [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Issue with getParserData in R3.0.0
Hello,
I am migrating my package lambda.r to R3.0.0 and am experiencing some issues
with the getParserData function (which replaces the parser package). Basically
the function works in the R shell but fails when either called from RUnit or
from R CMD check.
I've narrowed it down to the function getSrcfile, which is returning different
values depending on the code path. From the command line (works okay):
debug: srcfile <- getSrcfile(x)
Browse[2]>
debug: if (is.null(srcfile)) return(NULL) else data <- srcfile$parseData
Browse[2]> srcfile
When running from the Runit script I get this instead:
debug: srcfile <- getSrcfile(x)
Browse[3]>
debug: if (is.null(srcfile)) return(NULL) else data <- srcfile$parseData
Browse[3]> srcfile
NULL
Below is an example calling the getParserData from the command line:
> text <- "abs_max(a, b) %::% numeric:numeric:numeric"
> parse(text=text)
expression(abs_max(a, b) %::% numeric:numeric:numeric)
> getParseData(parse(text=text))
line1 col1 line2 col2 id parenttoken terminaltext
27 11 1 42 27 0 exprFALSE
14 11 1 13 14 27 exprFALSE
1 11 17 1 3 SYMBOL_FUNCTION_CALL TRUE abs_max
3 11 17 3 14 exprFALSE
2 18 18 2 14 '(' TRUE (
4 19 19 4 6 SYMBOL TRUE a
...
The RUnit call from the command line is
runTestFile('/home/brian/workspace/lambda.r/inst/unitTests/runit.dispatching.4.R')
and fails because of the NULL value of srcfile. The first line of the runit
test file is
abs_max(a, b) %::% numeric:numeric:numeric
Any insights are appreciated.
Brian
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Re: [Rd] Who does develop the R core and libs, and how / where is it hosted?
On Jan 14, 2013, at 6:32 PM, oliver wrote: > BTW: I looked up the string "wish list" in some of the mentioned docs > (mentioned in this thread) > but did not found it. > Can you please point me to it directly? > Googling for "R wish list" brings me links to a producer of toys. > > Or did you mean I should ask R users for their wishes??! > > (Some R users - on this list - asked for Julia language as a speedup > alternative for R a while ago ) Is this what you're looking for: http://developer.r-project.org/ (see TODO lists) > All in all it seems like no special things need to be done. > The FSF for example has a page where they ask for support in certain areas, > so, this looks rather urgent. > R seems not to have such urgent needs for support How about cleaning up some of the documentation/wiki pages? [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Issue with getParserData in R3.0.0
Thanks that seems to work. It looks like other packages explicitly change this
to FALSE, so I have to set this to TRUE for each function call. Is there any
particular policy for packages that update this option? Should I restore the
original value upon function exit?
Warm Regards,
Brian
On Jan 14, 2013, at 9:34 AM, Duncan Murdoch wrote:
> On 13-01-13 8:43 PM, Brian Lee Yung Rowe wrote:> Hello,
> >
> > I am migrating my package lambda.r to R3.0.0 and am experiencing some
> > issues with the getParserData function (which replaces the parser package).
> > Basically the function works in the R shell but fails when either called
> > from RUnit or from R CMD check.
> >
> > I've narrowed it down to the function getSrcfile, which is returning
> > different values depending on the code path. From the command line (works
> > okay):
> >
> > debug: srcfile <- getSrcfile(x)
> > Browse[2]>
> > debug: if (is.null(srcfile)) return(NULL) else data <- srcfile$parseData
> > Browse[2]> srcfile
> >
> >
> > When running from the Runit script I get this instead:
> > debug: srcfile <- getSrcfile(x)
> > Browse[3]>
> > debug: if (is.null(srcfile)) return(NULL) else data <- srcfile$parseData
> > Browse[3]> srcfile
> > NULL
> >
> >
> > Below is an example calling the getParserData from the command line:
> >> text <- "abs_max(a, b) %::% numeric:numeric:numeric"
> >> parse(text=text)
> > expression(abs_max(a, b) %::% numeric:numeric:numeric)
> >> getParseData(parse(text=text))
> > line1 col1 line2 col2 id parenttoken terminaltext
> > 27 11 1 42 27 0 exprFALSE
> > 14 11 1 13 14 27 exprFALSE
> > 1 11 17 1 3 SYMBOL_FUNCTION_CALL TRUE abs_max
> > 3 11 17 3 14 exprFALSE
> > 2 18 18 2 14 '(' TRUE (
> > 4 19 19 4 6 SYMBOL TRUE a
> > ...
> >
> > The RUnit call from the command line is
> > runTestFile('/home/brian/workspace/lambda.r/inst/unitTests/runit.dispatching.4.R')
> >
> > and fails because of the NULL value of srcfile. The first line of the runit
> > test file is
> >abs_max(a, b) %::% numeric:numeric:numeric
> >
> > Any insights are appreciated.
>
> I think in the case that is failing you just don't have any source info in
> the parse. parse() only installs it if the "keep.source" option is TRUE, and
> the default for that is the result of interactive(). So when you are not
> interactive you don't get source info.
>
> You can fix it by explicitly setting options(keep.source=TRUE).
>
> Duncan Murdoch
>
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Re: [Rd] Who does develop the R core and libs, and how / where is it hosted?
Maybe the master Bugzilla is what you are looking for instead: https://bugs.r-project.org/bugzilla3/buglist.cgi?quicksearch=wishlist On Jan 14, 2013, at 7:55 PM, Oliver Bandel wrote: > > > Am 15.01.2013 um 01:11 schrieb Brian Lee Yung Rowe : > >> >> On Jan 14, 2013, at 6:32 PM, oliver wrote: >> >>> BTW: I looked up the string "wish list" in some of the mentioned docs >>> (mentioned in this thread) >>> but did not found it. >>> Can you please point me to it directly? >>> Googling for "R wish list" brings me links to a producer of toys. >>> >>> Or did you mean I should ask R users for their wishes??! >>> >>> (Some R users - on this list - asked for Julia language as a speedup >>> alternative for R a while ago ) >> >> Is this what you're looking for: http://developer.r-project.org/ (see TODO >> lists) > > Ah, yes,there are TODO lists, thanks. > > This is at least some kind of thing yi was looking for. > But these are personell TODO lists. > Are their any goals for R as whole project? > > > >> >> >>> All in all it seems like no special things need to be done. >>> The FSF for example has a page where they ask for support in certain areas, >>> so, this looks rather urgent. >>> R seems not to have such urgent needs for support >> >> How about cleaning up some of the documentation/wiki pages? > > I'm not a friend of seperating design, coding, documentation, ... > > IMHO this should be something that is not seperated. > And I also think, that the way, R packages will be written > (code as well as documentation together) uses the same > kind of philosophy. > I was very happy about this close relation between code and > documentation,mthat is necessary to wrte a package. > > I thought the same holds true for R project as a whole. > So I maybe was wrong with this assumption. > > Ciao, >Olver > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Contract Syntactic Sugar
Ivo,
You might be interested in my lambda.r package which provides syntax (using the
%::% operator) for type constraints. Given a function with n arguments, the
type constraint requires n + 1 types, as the last type listed is the return
type. Lambda.r also provides syntax for specifying any arbitrary condition on
the input arguments via the %when% operator. For your example below you could
do the following:
exponentiate(x, exponent) %::% data.frame : numeric : numeric
exponentiate(x, exponent) %when% {
is.positive(x)
} %as% {
x$base ^ exponent
}
You can see more examples in the package (available on CRAN) or in the source
(https://github.com/muxspace/lambda.r).
HTH,
Brian
On Feb 4, 2013, at 4:53 PM, ivo welch wrote:
> ## the following is a dream: add some sugar syntax to allow for
> contracts with teeth (in and out checking)
>
>> is.positive <- function(x) (all(x>0))
>
>> exponentiate <- function( x ::is.data.frame , exponent ::is.numeric
>> is.positive) :: is.vector is.numeric {
>x$base :: is.positive## error also if base does not exist
> in x; may need some special IQ
>x$base^exponent
> }
>
> should be self-explanatory. anything that has '::' means "run what is
> before through all the functions after and barf if it is not true".
> any other operator rather than :: or other syntax would be as
> good---this is just illustratory. in the end, this code should be
> viewed by R as the same as
>
>> exponentiate <- function( x, exponent ) {
>stopifnot( is.data.frame(x) )
>stopifnot( is.numeric(exponent) )
>stopifnot( is.positive(exponent) )
>stopifnot( exists("base", "x") )
>stopifnot( is.positive( x$base ) )
>return.value <- x$base^exponent
>stopifnot( is.vector(return.value) )
>stopifnot( is.numeric(return.value) )
>return.value
> }
>
> is this a feasible summer project for a student with a prospect of
> inclusion of the completed code in the R core language itself if I pay
> for the development time? {or does better syntax already exist and I
> am just ignorant (which I often am)?}
>
> regards,
>
> /iaw
>
> Ivo Welch (ivo.we...@gmail.com)
>
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Re: [Rd] Contract Syntactic Sugar
Ivo,
If you don't like the multipart function syntax you can write a single
definition. Personally I prefer this as it isolates data management logic and
control flow from model/application logic. There are duck typing operators that
you can use in the guard similar to the syntax you wrote. You can also create
your own types and use that in a type constraint. However the type constraint
syntax must be a distinct statement although you could embed it all within a
guard. Here are three different approaches using lambda.r.
NaturalNumber(x) %when% {
all(is.positive(x))
} %as% { x }
# Using an explicit type constraint with a custom type
exponentiate(x, exponent) %::% data.frame : NaturalNumber : integer
exponentiate(x, exponent) %when% {
x %hasa% base
} %as% { x$base ^ exponent }
-- or --
# Embedding everything in a guard
exponentiate(x, exponent) %when% {
x %hasa% base
x %isa% NaturalNumber
} %as% { x$base ^ exponent }
-- or --
# Eschewing a custom type for explicit statements
exponentiate(x, exponent) %when% {
x %hasa% base
all(is.positive(x$base))
} %as% { x$base ^ exponent
Warm Regards,
Brian
•
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917 496 4583
On Feb 4, 2013, at 6:23 PM, ivo welch wrote:
> hi brian---interesting and very impressive. is it possible to move
> everything into one definition and/or to chain multiple conditions?
>
> exponentiate(x, exponent) %::% data.frame : c(numeric,allpositive) :
> integer %as% {
> x %has% base ## my invention, since this is not checked, and R is
> not strict enough
> x$base %::% allpositive
> x$base ^ exponent
> }
>
> multiple creations as in your doc examples on the same function are a
> recipe for errors for me. it's also why I am not too fond of
> TypeInfo. chaining conditions in my c() is not important, as long as
> I can define my own types (which can check multiple aspects at the
> same time). suggestion: in your doc example, can you define a
> different type than an integer? it's a little confusing. how about
> defining a strictly positive integer?
>
> regards,
>
> /iaw
>
> Ivo Welch (ivo.we...@gmail.com)
> http://www.ivo-welch.info/
> J. Fred Weston Professor of Finance
> Anderson School at UCLA, C519
> Director, UCLA Anderson Fink Center for Finance and Investments
> Free Finance Textbook, http://book.ivo-welch.info/
> Editor, Critical Finance Review, http://www.critical-finance-review.org/
>
>
>
> On Mon, Feb 4, 2013 at 2:10 PM, Brian Lee Yung Rowe wrote:
>> Ivo,
>>
>> You might be interested in my lambda.r package which provides syntax (using
>> the %::% operator) for type constraints. Given a function with n arguments,
>> the type constraint requires n + 1 types, as the last type listed is the
>> return type. Lambda.r also provides syntax for specifying any arbitrary
>> condition on the input arguments via the %when% operator. For your example
>> below you could do the following:
>>
>> exponentiate(x, exponent) %::% data.frame : numeric : numeric
>> exponentiate(x, exponent) %when% {
>> is.positive(x)
>> } %as% {
>> x$base ^ exponent
>> }
>>
>> You can see more examples in the package (available on CRAN) or in the
>> source (https://github.com/muxspace/lambda.r).
>>
>> HTH,
>> Brian
>>
>>
>> On Feb 4, 2013, at 4:53 PM, ivo welch wrote:
>>
>>> ## the following is a dream: add some sugar syntax to allow for
>>> contracts with teeth (in and out checking)
>>>
>>>> is.positive <- function(x) (all(x>0))
>>>
>>>> exponentiate <- function( x ::is.data.frame , exponent ::is.numeric
>>>> is.positive) :: is.vector is.numeric {
>>> x$base :: is.positive## error also if base does not exist
>>> in x; may need some special IQ
>>> x$base^exponent
>>> }
>>>
>>> should be self-explanatory. anything that has '::' means "run what is
>>> before through all the functions after and barf if it is not true".
>>> any other operator rather than :: or other syntax would be as
>>> good---this is just illustratory. in the end, this code should be
>>> viewed by R as the same as
>>>
>>>> exponentiate <- function( x, exponent ) {
>>> stopifnot( is.data.frame(x) )
>>> stopifnot( is.numeric(exponent) )
>>> stopifnot( is.positive(exponent) )
>>> stopifnot( exists("base", "x") )
>>> stopifnot( is.positive( x$base ) )
>>> return.value <- x$base^exponent
>>> stopifnot( is.vector(return.value) )
>>> stopifnot( is.numeric(return.value)
Re: [Rd] Regression stars
I thought that the default was the way it was for performance reasons. For
large data.frames or repeated applications, using factors should be faster for
non-trivial strings.
> fs <- c('apple','peach','watermelon','spinach','persimmon','potato','kale')
> n <- 100
>
> a1 <- data.frame(f=sample(fs,n,replace=TRUE), x1=rnorm(n), x2=rnorm(n),
> stringsAsFactors=TRUE)
> a2 <- data.frame(f=sample(fs,n,replace=TRUE), x1=rnorm(n), x2=rnorm(n),
> stringsAsFactors=FALSE)
>
> fn <- function(i,x) x[x$f %in% c('kale','spinach'),]
> system.time(z <- sapply(1:100, fn, a1))
user system elapsed
19.614 4.037 24.649
> system.time(z <- sapply(1:100, fn, a2))
user system elapsed
19.726 7.715 36.761
On Feb 12, 2013, at 10:40 AM, Ben Bolker wrote:
>
> Thanks, Uwe.
> Now let me go one step farther.
>
> Can you (or anyone) give a good argument **other than backward
> compatibility** for keeping the stringAsFactors=TRUE argument on
> data.frame()?
>
> I appreciate your distinction between data.frame() and read.table()'s
> use of stringAsFactors, and I can see that there is some point for
> quick-and-dirty interactive use in setting all non-numeric variables to
> factors (arguing that wanting non-numerics as factors is somewhat more
> common than wanting them as strings).
>
> It might be nice to add an optional stringsAsFactors (and check.names)
> argument to transform(): I've had to write my own Transform() function
> to allow the defaults to be overridden, since transform() calls
> data.frame() with the defaults. (Setting the stringsAsFactors option
> globally would work, although not for check.names.)
>
> Ben BOlker
>
>>
>>>
What I will likely do is
make a few changes so that character vectors are automatically changed
to factors in modelling functions, so that operating with
stringsAsFactors=FALSE doesn't trigger silly warnings.
Duncan Murdoch
>>>
>>> [apologies for snipping context: "gmane made me do it"]
>>>
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>>>
>
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Re: [Rd] Suppress specific warnings
For my logging package (futile.logger) any log statements coming from a package
are assigned to a package namespace. This way you have control of log messages
at a package level (e.g. I can set the default log threshold to DEBUG, while
package 'A' has a log threshold of WARN).
I seems a hierarchical namespace facility would work for the below case as
well.
On Apr 18, 2013, at 9:29 AM, Martin Morgan wrote:
>> To suppress just this one, try this:
>>
>> withCallingHandlers(x + 1:3,
>>warning=function(w) {
>> if (grepl("longer object length", w$message))
>> invokeRestart("muffleWarning")
>>} )
>
> ...which are then caught as
>
> withCallingHandlers({
> warning(w) # 'curves'; caught
> warning("another warning")
> }, curves=function(w) invokeRestart("muffleWarning"))
>
> The tricky part is to come up with an appropriate scheme for classifying
> warnings.
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Re: [Rd] Patch proposal for R style consistency (concerning deparse.c)
Writing R in a declarative style a la functional programming makes this whole
thread go away since you don't need if/else blocks.
•
Brian Lee Yung Rowe
On May 2, 2013, at 8:27 AM, Terry Therneau wrote:
> I'll be the "anybody" to argue that
> } else {
> is an ugly kludge which you will never find in my source code. Yes, it's
> necessary at the command line because the parser needs help in guessing when
> an expression is finished, but is only needed in that case. Since I can
> hardly imagine using else at the command line (that many correct characters
> in a row exceeds my typing skill) it's not an issue for me. I most certainly
> would not inflict this construction on my pupils when teaching a class, nor
> that any break of a long line has to be after "+" but not before, nor other
> crutches for the parser's sake. Let them know about the special case of
> course, but don't sacrifice good coding style the deficiency.
>
> That said, I am completely ambivalent to the result of deparse. Just
> throwing up an objection to the "purity" argument: things were beginning to
> sound a bit too bombastic :-).
>
> Terry T.
>
> On 05/02/2013 05:00 AM, r-devel-requ...@r-project.org wrote:
>> I want "} else {". Yihue wants "} else {". And I have not heard anybody
>> say they prefer the other way, unless you interpret Duncan's comment
>> "that's nonsense" as a blanket defense of the status quo. But I don't think
>> he meant that. This is a matter of style consistency and avoidance of new
>> R-user confusion and error.
>
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