[Rd] S4 coercion responsibility
Should functions or the user be responsible for coercing an S4 object
argument containing the proper object (and thus should below be
considered a bug in the packages or not)?
The example is with RSQLite but the same thing happens with RMySQL, and
other DBI packages.
> library("RSQLite") Loading required package: DBI
> m <- dbDriver("SQLite")
> con <- dbConnect(m)
> setClass("SQLConPlus", contains=c("SQLiteConnection","integer"))
[1] "SQLConPlus"
> conPlus <- new("SQLConPlus", con, 1)
> dbListTables(con)
character(0)
> dbListTables(conPlus)
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (invalid dbManager handle)
> dbListTables(as(conPlus, "SQLiteConnection"))
character(0)
>
The problem is happening in sqliteExecStatement which does
conId <- as(con, "integer")
but con only *contains* an SQLiteConnection and the other integer
causes confusion. If the line were
conId <- as(as(con, "SQLiteConnection"), "integer")
everything works.
I can work around this, but I am curious where responsibility for this
coercion should be.
Paul Gilbert
La version française suit le texte anglais.
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[Rd] Including data in package for use by C functions
How should one go about including data files for use by some C function in an R package? The data subdirectory is for additional data files the package makes available for loading from R, not C, and including the files in some other directory is no good because non- standard directories are removed when building the package. Thanks, E __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Including data in package for use by C functions
On 9/15/2008 10:18 AM, Ernest Turro wrote: How should one go about including data files for use by some C function in an R package? The data subdirectory is for additional data files the package makes available for loading from R, not C, and including the files in some other directory is no good because non- standard directories are removed when building the package. Nonstandard directories in the "inst" subdir are moved up one level and kept, so that's the place to put stuff like this. e.g. packagesrc/inst/foo becomes package/foo when the package is installed. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Cross-platform function availability
Hi all, Is there any way to determine which functions are available on which platforms? For example, winProgr essBar (and related functions) are only available on Windows, but what about tkProgressBar and txtProgressBar? Is there any way to figure out which functions are only available on certain platforms, without installing R on that platform and checking? Thanks, Hadley -- http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Cross-platform function availability
On 9/15/2008 11:42 AM, hadley wickham wrote: Hi all, Is there any way to determine which functions are available on which platforms? For example, winProgr essBar (and related functions) are only available on Windows, but what about tkProgressBar and txtProgressBar? Is there any way to figure out which functions are only available on certain platforms, without installing R on that platform and checking? Generally I think the only reliable way is to look at the source. Things in "windows" subdirs, or marked off with "#ifdef windows" (in Rd) or "#ifdef Win32" (in C) are for windows only. Probably our documentation should point out when something is platform-specific, and frequently it does, but I don't think it is completely consistent in this. Duncan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Cross-platform function availability
I think it is a little more complex than just installing and checking. tkProgressBar uses tcltk which works on the major platforms (unix/linux, mac, windows), but only if tk is installed and available. I believe that on mac tk is only available if X11 is used and if I remember correctly, if R is run by clicking an icon, then X11 is not used (but it is if run from a command window). So checking may say it does not work (when it does in a different way), or that it does work, but the end user may not get it to work. I believe that txtProgressBar works on any version that can produce text (all that I know of), but you may get some funny results if output is being sent directly to a file. More generally, from the packages link on your favorite CRAN mirror, there is a link to package test results that show the results of testing the packages on different platforms that may give some idea if the function works on the tested platforms (if the documentation for the function has examples not wrapped in dontrun commands or other tests). Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of hadley wickham > Sent: Monday, September 15, 2008 9:43 AM > To: r-devel@r-project.org > Subject: [Rd] Cross-platform function availability > > Hi all, > > Is there any way to determine which functions are available > on which platforms? For example, winProgr essBar (and > related functions) are only available on Windows, but what > about tkProgressBar and txtProgressBar? Is there any way to > figure out which functions are only available on certain > platforms, without installing R on that platform and checking? > > Thanks, > > Hadley > > -- > http://had.co.nz/ > > __ > 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] S4 coercion responsibility
* On 2008-09-15 at 08:56 -0400 Paul Gilbert wrote:
> Should functions or the user be responsible for coercing an S4 object
> argument containing the proper object (and thus should below be
> considered a bug in the packages or not)?
>
> The example is with RSQLite but the same thing happens with RMySQL, and
> other DBI packages.
>
> > library("RSQLite") Loading required package: DBI
> > m <- dbDriver("SQLite")
> > con <- dbConnect(m)
> > setClass("SQLConPlus", contains=c("SQLiteConnection","integer"))
> [1] "SQLConPlus"
> > conPlus <- new("SQLConPlus", con, 1)
> > dbListTables(con)
> character(0)
> > dbListTables(conPlus)
> Error in sqliteExecStatement(con, statement, bind.data) :
> RS-DBI driver: (invalid dbManager handle)
> > dbListTables(as(conPlus, "SQLiteConnection"))
> character(0)
> >
>
> The problem is happening in sqliteExecStatement which does
> conId <- as(con, "integer")
> but con only *contains* an SQLiteConnection and the other integer
> causes confusion. If the line were
> conId <- as(as(con, "SQLiteConnection"), "integer")
> everything works.
>
> I can work around this, but I am curious where responsibility for this
> coercion should be.
Well, you've created a class that is-a SQLiteConnection *and* is-a
integer. The fact that the as() method dispatch doesn't match that of
SQLiteConnection should really be that surprising.
I don't see how this could be the responsibility of the author of the
class you've subclassed.
I would also question why SQLConPlus is extending integer. That seems
like a very strange choice. Why not extend SQLiteConnection and add
extra slots as you like. The dispatch will in this case be much
easier to reason about.
+ seth
--
Seth Falcon | http://userprimary.net/user/
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Re: [Rd] Using R from Java
Hi, Take a look at the rJava package. It includes JRI that lets you call R from Java. From the README: This package contains code that is necessary to run R as a single thread of a Java application. It provides callback that make it possible to run R in REPL mode thus giving the Java application full access to the console. Currently the API is very, very low-level, comparable to the C level interface to R. Convenience methods for mid to high-level are planned, but not implemented yet. Good luck, Lars Marzio Sala wrote: Hello, I am interesting in using R from a web application, for basic statistics and plots. The server is Java-based (tomcat). The simplest solution is a system call that generates the text or the image, then the servlet forwards the output. This can be done from any language, but it is quite inelegant and slow for the initialization time. Is there any package or approach for accessing R from a Java servlet you can suggest? Thanks in advance for any suggestion. Regards, -Marzio __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Cross-platform function availability
On Mon, Sep 15, 2008 at 12:06 PM, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > On 9/15/2008 11:42 AM, hadley wickham wrote: >> >> Hi all, >> >> Is there any way to determine which functions are available on which >> platforms? For example, winProgr essBar (and related functions) are >> only available on Windows, but what about tkProgressBar and >> txtProgressBar? Is there any way to figure out which functions are >> only available on certain platforms, without installing R on that >> platform and checking? > > Generally I think the only reliable way is to look at the source. Things in > "windows" subdirs, or marked off with "#ifdef windows" (in Rd) or "#ifdef > Win32" (in C) are for windows only. Probably our documentation should point > out when something is platform-specific, and frequently it does, but I don't > think it is completely consistent in this. To me it seems like it would be easier to include the all functions all on platforms, and then return an error on platforms where they aren't supported. The problem I'm now having is that I'm now getting an warning when building my package because it can't link to the documentation for winProgressBar. Should I just ignore that warning? Hadley -- http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Cross-platform function availability
On 9/15/2008 1:43 PM, hadley wickham wrote: On Mon, Sep 15, 2008 at 12:06 PM, Duncan Murdoch <[EMAIL PROTECTED]> wrote: On 9/15/2008 11:42 AM, hadley wickham wrote: Hi all, Is there any way to determine which functions are available on which platforms? For example, winProgr essBar (and related functions) are only available on Windows, but what about tkProgressBar and txtProgressBar? Is there any way to figure out which functions are only available on certain platforms, without installing R on that platform and checking? Generally I think the only reliable way is to look at the source. Things in "windows" subdirs, or marked off with "#ifdef windows" (in Rd) or "#ifdef Win32" (in C) are for windows only. Probably our documentation should point out when something is platform-specific, and frequently it does, but I don't think it is completely consistent in this. To me it seems like it would be easier to include the all functions all on platforms, and then return an error on platforms where they aren't supported. The problem I'm now having is that I'm now getting an warning when building my package because it can't link to the documentation for winProgressBar. Should I just ignore that warning? It's better not to ignore warnings. I'd suggest wrapping the link in "#ifdef windows" (assuming it's in an Rd file). Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Typo in cut.Rd
In the \seealso section of cut.Rd, can "\pkg{hmisc}" be changed to
"\pkg{Hmisc}"?
Thanks,
Stephen
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Re: [Rd] Typo in cut.Rd
On 15/09/2008 5:45 PM, Stephen Weigand wrote:
In the \seealso section of cut.Rd, can "\pkg{hmisc}" be changed to
"\pkg{Hmisc}"?
Thanks, I'll fix it.
Duncan Murdoch
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[Rd] odesolve dynload example
Hello R Developers,
This is my first foray into using c-code with R, so please forgive my
foolishness.
I had a look at the archives and did not find anything on this, so
hopefully I am not doubling up.
I have tried to use R cmd to create an object file from the odesolve
dynload example.
I am using windows and have just installed rtools, and have the latest
version of stable R (2..7.2).
This is what happened:
C:\Program Files\R\R-2.7.2\library\odesolve\dynload\c>Rcmd SHLIB mymod.c
making mymod.d from mymod.c
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I
C:/PROGRA~1/R/R-27~1.2/include -i mymod_res.rc -o mymod_res.o
gcc -std=gnu99 -shared -s -o mymod.dll mymod.def mymod.o mymod_res.o
-LC:/PROGRA~1/R/R-27~1.2/bin-lR
Cannot export myderivs: symbol not found
Cannot export myjac: symbol not found
Cannot export mymod: symbol not found
mymod.o: In function `mymod':
/home/setzer/tasks/Programming_Projects/odesolve/odesolve/inst/dynload/c
/mymod.c:14: undefined reference to `GLOBAL_OFFSET_TA
BLE_'
mymod.o: In function `myderivs':
/home/setzer/tasks/Programming_Projects/odesolve/odesolve/inst/dynload/c
/mymod.c:21: undefined reference to `GLOBAL_OFFSET_TA
BLE_'
mymod.o: In function `myjac':
/home/setzer/tasks/Programming_Projects/odesolve/odesolve/inst/dynload/c
/mymod.c:30: undefined reference to `GLOBAL_OFFSET_TA
BLE_'
collect2: ld returned 1 exit status
make: *** [mymod.dll] Error 1
Any ideas what I have not got set up properly? What do I need to do to
get this firing?
Advice appreciated.
Kind regards,
Matt Redding
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[Rd] question in value-based color in image()
Hello, I have a matrix with value varying from -1 to 1. I hope to use scaled color based on its value to produce an image of this matrix. Suppose I hope to label those data in [-1,-0.5] with blue, label those [-0.5,0.8] with light blue (tone is proportional to its value) and label those [0.8,1] with white. How can I use image() and rgb() to achieve this? It would be great if I can have a color scale legend, too. TIA, Chris [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] odesolve dynload example
Redding, Matthew wrote: Hello R Developers, This is my first foray into using c-code with R, so please forgive my foolishness. I had a look at the archives and did not find anything on this, so hopefully I am not doubling up. I have tried to use R cmd to create an object file from the odesolve dynload example. I am using windows and have just installed rtools, and have the latest version of stable R (2..7.2). This is what happened: C:\Program Files\R\R-2.7.2\library\odesolve\dynload\c>Rcmd SHLIB mymod.c making mymod.d from mymod.c windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I C:/PROGRA~1/R/R-27~1.2/include -i mymod_res.rc -o mymod_res.o gcc -std=gnu99 -shared -s -o mymod.dll mymod.def mymod.o mymod_res.o -LC:/PROGRA~1/R/R-27~1.2/bin-lR Cannot export myderivs: symbol not found Cannot export myjac: symbol not found Cannot export mymod: symbol not found mymod.o: In function `mymod': /home/setzer/tasks/Programming_Projects/odesolve/odesolve/inst/dynload/c /mymod.c:14: undefined reference to `GLOBAL_OFFSET_TA BLE_' mymod.o: In function `myderivs': /home/setzer/tasks/Programming_Projects/odesolve/odesolve/inst/dynload/c /mymod.c:21: undefined reference to `GLOBAL_OFFSET_TA BLE_' mymod.o: In function `myjac': /home/setzer/tasks/Programming_Projects/odesolve/odesolve/inst/dynload/c /mymod.c:30: undefined reference to `GLOBAL_OFFSET_TA BLE_' collect2: ld returned 1 exit status make: *** [mymod.dll] Error 1 Any ideas what I have not got set up properly? What do I need to do to get this firing? Advice appreciated. I'm a bit rusty on the windows tools, but it looks like mymod.o and mymod_res.rc not being made above. Any chance that you have old versions lying around? -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
