Re: [Rd] Ignore user interrupts
Sharpie wrote
evalWithoutInterrupts - function(expr, envir = parent.frame())
{
.Call(do_evalWithoutInterrupts, expr, envir)
}
With a C-level implemention:
SEXPR do_evalWithoutInterrupts(SEXP expr, SEXP envir)
{
SEXP result;
BEGIN_SUSPEND_INTERRUPTS{
result = eval(expr, envir);
}END_SUSPEND_INTERRUPTS;
return result;
}
Some more info, and a possible bug:
This approach appears to work if I change `evalWithoutInterrupts` so that it
invokes `substitute` on `expr` before passing to the C code:
evalWithoutInterrupts - function(expr, envir = parent.frame())
{
.Call(do_evalWithoutInterrupts, substitute(expr), envir)
}
For example, I can do the following (using OS X, R 2.14.1 in Terminal.app):
eval({for(i in 1:1000){log(i)};message(Hello, world!)})
evalWithoutInterrupts({for(i in 1:1000){log(i)};message(Hello,
world!)})
The `eval` call can be interrupted by CTRL-C as normal. However, with the
`evalWithoutInterrupts` call, I can tap on CTRL-C and the loop will still
execute, Hello, world! will be printed and then the interrupt will be
registered:
evalWithoutInterrupts({for(i in 1:1000){log(i)};message(Hello,
world!)})
^C^C^C^C^CHello, world!
The only odd thing I came across was when I tried to test this function
using `Sys.sleep` instead of a long loop:
evalWithoutInterrupts(Sys.sleep(3);message(Hello, world!)})
The call can be interrupted immediately by CTRL-C. Some poking in GDB
reveals that the call chain passes from my C function
`evalWithoutInterrupts` to `do_syssleep` an finally to `Rf_onintr` through
`R_checkActivity`:
Breakpoint 1, Rf_onintr () at errors.c:123
123 if (R_interrupts_suspended) {
(gdb) bt
#0 Rf_onintr () at errors.c:123
#1 0x0001001ced41 in R_SelectEx (n=1, readfds=0x10038cdc0,
writefds=0x0, exceptfds=0x0, timeout=0x7fff5fbf8b60, intr=0) at
sys-std.c:127
#2 0x0001001cf109 in R_checkActivityEx (usec=300, ignore_stdin=1,
intr=0) at sys-std.c:329
#3 0x0001001cf14b in R_checkActivity (usec=300, ignore_stdin=1) at
sys-std.c:338
#4 0x0001001d0fbb in do_syssleep (call=0x1025bb200, op=0x10086d0d8,
args=0x1033679b8, rho=0x1033679f0) at sys-std.c:1299
#5 0x0001000c7608 in bcEval (body=0x1025ba878, rho=0x1033679f0,
useCache=TRUE) at eval.c:4445
#6 0x0001000bcb69 in Rf_eval (e=0x1025ba878, rho=0x1033679f0) at
eval.c:401
#7 0x0001000bddd7 in Rf_applyClosure (call=0x103366e38, op=0x1025ba8e8,
arglist=0x103367a60, rho=0x100877ea8, suppliedenv=0x100877ee0) at eval.c:840
#8 0x0001000bd22e in Rf_eval (e=0x103366e38, rho=0x100877ea8) at
eval.c:515
#9 0x0001000bf879 in do_begin (call=0x103366ee0, op=0x10084e6e0,
args=0x103366dc8, rho=0x100877ea8) at eval.c:1422
#10 0x0001000bcf40 in Rf_eval (e=0x103366ee0, rho=0x100877ea8) at
eval.c:471
#11 0x000102fc736d in evalWithoutInterrupts ()
However, at this point the variable `R_interrupts_suspended` is not set to
`TRUE` as I would expect due to the `BEGIN_SUSPEND_INTERRUPTS` block in
`evalWithoutInterrupts`:
(gdb) p R_interrupts_suspended
$1 = FALSE
Bug?
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
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Re: [Rd] Non-default build options
Dirk Eddelbuettel wrote b) having BLAS as a defined interface is wonderful for swapping default (unaccelerated) BLAS for accelerated BLAS like Atlas, Goto, OpenBLAS, MKL, ... Several of these BLAS have in fact been available for either Debian or Ubuntu in some form (sometimes involving a helper script as eg Goto could never be part of an FLOSS distro). Just an aside: Goto BLAS is now available under the BSD license, so it should be perfectly acceptable to include in a FLOSS distribution. However, development has ceased so Goto will probably loose it's edge as new CPU families are shipped. -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/Non-default-build-options-tp4328512p4329615.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
[Rd] Ignore user interrupts
Is there a way to suspend user interrupts for the duration of a function call? There is a point in one of my packages where values are being written to a Filehash database. If the user is unlucky enough to send an interrupt while this code is active, then they have to: - Hunt down a lock file and dispose of it before the package will work again. - Possibly trash the Filehash database and start over if the interrupt caused R to leave the database file in a corrupted state. Is there something analogous to the C macros BEGIN_SUSPEND_INTERRUPTS/END_SUSPEND_INTERRUPTS that I can use at the R level to delay interrupts until after critical code has executed? If not, would it work to move the function call into a C function that uses `eval` inside a block protected by BEGIN_SUSPEND_INTERRUPTS? -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/Ignore-user-interrupts-tp4321252p4321252.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
Re: [Rd] Ignore user interrupts
Sharpie wrote
If not, would it work to move the function call into a C function that
uses `eval` inside a block protected by BEGIN_SUSPEND_INTERRUPTS?
Just to clarify, if there is no functionality at the R level for evaluating
an expression without interrupts, would it be possible to create it by
defining a function:
evalWithoutInterrupts - function(expr, envir = parent.frame())
{
.Call(do_evalWithoutInterrupts, expr, envir)
}
With a C-level implemention:
SEXPR do_evalWithoutInterrupts(SEXP expr, SEXP envir)
{
SEXP result;
BEGIN_SUSPEND_INTERRUPTS{
result = eval(expr, envir);
}END_SUSPEND_INTERRUPTS;
return result;
}
Would that be a correct way to tackle the problem?
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
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Re: [Rd] Inconsistencies in device_Raster when axes are reflected
Paul Murrell wrote
I think the problem is that I just failed to anticipate this situation
(i.e., the current documentation and behaviour both assume xlim[1]
xlim[2] and ylim[1] ylim[2]).
Will take a look at where to apply a fix (EITHER allow the API to be
more flexible [allow negative 'width' and 'height' and 'x' and 'y' to be
other than left-bottom], which will require complicating the code in
some devices OR keep the API fixed and complicate the graphics engine
code instead). The rotation argument adds an interesting twist ...
Thanks for the report!
Paul
Thanks for the reply Paul!
This isn't too hard to handle at the device level. For example, all I had to
do to the tikzDevice was add a loop and some logic that re-ordered the
raster vector and re-positioned the coordinate anchor:
int i, j, index, target, row_offset = 0, col_offset = 0, row_trans = 1,
col_trans = 1;
if ( height 0 ) {
/* Using these parameters, one can cause a loop to count backwards */
row_trans = -1;
row_offset = h - 1;
/*
* If a dimension is negative, the (x,y) coordinate no longer references
* the lower left corner of the image. We correct for this and then make
* sure the dimension is positive.
*/
y += height;
height = fabs(height);
}
if ( width 0 ) {
col_trans = -1;
col_offset = w - 1;
x += width;
width = fabs(width);
}
for ( i = 0; i h; ++i ) {
for ( j = 0; j w; ++j ) {
target = i*w + j;
index = (row_trans*i + row_offset)*w + (col_trans*j + col_offset);
INTEGER(red_vec)[target] = R_RED(raster[index]);
INTEGER(green_vec)[target] = R_BLUE(raster[index]);
INTEGER(blue_vec)[target] = R_GREEN(raster[index]);
INTEGER(alpha_vec)[target] = R_ALPHA(raster[index]);
}
}
This gives the device the same behavior as the PDF device. So, the behavior
isn't too difficult to correct on the device end---I was just concerned by
the difference between documentation and behavior and wanted to make sure
the graphics engine was not expecting something different.
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
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[Rd] Inconsistencies in device_Raster when axes are reflected
I noticed some undocumented and inconsistent behavior in device_Raster when a plot is produced with reflected axes such as: image(volcano, xlim = c(1,0), useRaster = TRUE) image(volcano, ylim = c(1,0), useRaster = TRUE) The `pdf` device will perform horizontal and vertical reflections, while `quartz` will ignore the transformations when plotting to the screen, but when plotting to a file, `quartz(file = 'test.pdf', type = 'pdf')`, it will produce horizontal reflections and ignore vertical ones. When the `xlim` or `ylim` is reversed, negative widths and heights are passed to the C function `device_Raster`, which is not a behavior documented in `R_ext/GraphicsDevice.h`. Also, the values of `x` and `y` passed to `device_Raster` will be shifted by the width or height of the image such that the coordinates no longer reference the bottom-left corner of the image as `R_ext/GraphicsDevice.h` says they should. Given the inconsistencies in documentation and behavior, I am wondering what the intended behavior of `device_Raster` is in this situation. Thanks! -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/Inconsistencies-in-device-Raster-when-axes-are-reflected-tp4286320p4286320.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
Re: [Rd] Command completion of the R binary / Ubuntu
Deepayan Sarkar-3 wrote I believe only Debian/Ubuntu package it (and this would have been more appropriate for r-sig-debian). I'll coordinate with Dirk et al to update the relevant files. -Deepayan The bash completion script is also used by the Homebrew package manager on OS X. -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/Command-completion-of-the-R-binary-Ubuntu-tp4285040p4286476.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
Re: [Rd] matrix multiplication speed R
aftar wrote: Hi Can we use BLAS in R X64 for windows? Regards Aftar You are already using BLAS in R as R includes its own BLAS library. On Windows the 64-bit DLL is located at R_HOME\bin\x64\Rblas.dll. If you are asking about swapping that out for an optimized BLAS, you will probably have to: 1. Obtain and build an optimized BLAS such as ATLAS, Goto BLAS or Intel MKL 2. Build your own copy of R from source that links against this new blas. If there is a simpler way, I'm sure someone will correct me. - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/matrix-multiplication-speed-R-tp3217257p3510979.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
Re: [Rd] fortan common block
Paul Gilbert wrote: Is it possible in R to call a fortran routine that sets variables in a common block and expect the values to persist when a call is made from R to a second routine that uses the common block? If not (as I suspect), is it possible to use a common block in a group of routines that are used together, for as long the routines do not return to R? Paul Don't see why not--should be pretty easy to test. Personally, I would use variables in a Fortran 90 module over a common block. -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/fortan-common-block-tp3503204p3506373.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
Re: [Rd] Curry: proposed new functional programming, er, function.
Byron Ellis-2 wrote:
Hi all (especially R-core) I suppose,
With the introduction of the new functional programming functions into
base I thought I'd ask for a Curry() function. I use a simple one that
looks this:
Curry = function(FUN,...) { .orig = list(...);function(...)
do.call(FUN,c(.orig,list(...))) }
...
I would like to see this as well---it is one of the functional programming
constructs I really miss in R after playing with languages like Haskell.
Currently, the only Curry implementation I know of is in the roxygen package
which is kind of a weird dependency to install just for this one function.
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
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Re: [Rd] Wishlist: write R's bin path to the PATH variable and remove the version string in the installation dir under Windows
Yihui Xie-2 wrote: Hi, I guess this issue must have been brought forward long time ago, but I still hope you can consider under Windows (during installation): 1. put R's bin path in the PATH variable of the system so that we can use the commands R and Rscript more easily; On one hand it certainly would be nice to have this as an option similar to what the RTools installer does. For the 32/64 bit decision, perhaps RHOME/bin could be placed on the PATH and bin/R.exe turned into a bin/R.bat that calls bin/i386/R.exe, bin/x64/R.exe depending on the Windows architecture. On the other hand, the grizzled developer in me is saying this is a teaching moment. If someone is using a programming language they should know what an environment variable is and how to set it. Admittingly, setting environment variables is a PITA on Windows compared to UNIX. Here's a great freeware tool I have found that makes it so much easier: http://www.rapidee.com Another issue is that many Windows machines are locked down in such a way that environment variables cannot be set permanently. To deal with this, I carry a USB stick that has R installed on it and a batch script that `setx`es environment variables for me. Combined with an `autorun.inf` script, this basically lets me plug my USB stick into a Windows machine and get to work without worrying about how careful the sysadmin was when they set up the tools I like to use (or if they even bothered to include the tools I like to use). A good video tutorial for setting up autorun.inf from Tinkernut.com: http://www.youtube.com/watch?v=lFlgddjOPpw Some of the things in that video are outdated and the overall goal is to show how they could be used for nefarious purposes, but the part about converting a `.bat` script to a `.exe` binary and setting up an autorun.inf to execute the result is solid. Combine with MikTeX Portable and you should be able to Sweave from anywhere. Yihui Xie-2 wrote: 2. remove the version string like R-2.13.0 in the default installation directory, e.g. only use a directory like C:/Program Files/R/ instead of C:/Program Files/R/R-2.13.0/; I know many people just follow the default setting when installing R, and this version string will often lead to many (unnecessary) copies of R in the system and brings difficulty to the first issue (several possible bin directories); I'm aware of some existing efforts in overcoming the difficulty of calling R under Windows like the R batch files project (http://code.google.com/p/batchfiles/), but I believe this is better to be solved in R directly. As a package developer I rather like this---I can have multiple versions of R installed and easily set up my testsuite such that it loops through each one and executes the tests. -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/Wishlist-write-R-s-bin-path-to-the-PATH-variable-and-remove-the-version-string-in-the-installation-ds-tp3493922p3496533.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
[Rd] Source for bash_completion.d/R?
Hello, I was just tweaking the R build for the Homebrew package manager and I thought it would be nice to enable bash completion. I noticed that Debian-based systems install `/etc/bash_completion.d/R` but could not find a source for this file in the `etc` folder of the R source. Is the R bash completion script publicly available somewhere so that it could be pulled in by curl? - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/Source-for-bash-completion-d-R-tp3490662p3490662.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
Re: [Rd] FW: [Rcpp-devel] Question on 5.6 Interfacing C++ code
, C++ and Fortran programs to be stored as text strings at the R level and then dynamically compiled, loaded and interfaced. Could be along the lines of what you were thinking about with building dynamic compilation and execution options. - Also, it is always fun to drop by the Omegahat project (www.omegahat.org) and see what Duncan Temple Lang has been cooking up. He has a couple of packages for interfacing R with compiled code via LibFFI (rather than the built in pointer method you observed) and one package that has the beginnings of some LLVM bindings. -Charlie On 4/21/11 10:02 PM, Sharpie lt;ch...@sharpsteen.netgt; wrote: smcguffee wrote: You are right, I looked and I did find the R source code. However, it's largely written in R! I mean, I don't know how to trace the R code where INSTALL is recognized and follow it to a c or c++ level command. For example these are hits in .R files, not c files, and I don't know how to connect ... If you could point me to the functions that are called a c or c++ level, I'd love to see what R is doing for myself. Thanks! Sean Hi Sean! Along with many other people in this thread, I would strongly recommend a top-down approach to this. Build a package, stick some stuff in the src folder, run R CMD INSTALL on it and see what happens. The reason I recommend this approach is that it lets you focus on writing a package that does something useful rather than the nuts and bolts of cross platform compilation and installation. R CMD INSTALL takes care of this for you automagically and it is very good at what it does. I wrote a post some time back about building an example package from scratch that contains C code: http://r.789695.n4.nabble.com/Writing-own-simulation-function-in-C-td1580190.h tml#a1580423 It begins with the using the package.skeleton() function to kickstart things, discusses how to make sure the compiled code is dynamically loaded when a user runs library(your_package) and even discusses how to call R functions from inside of C functions and vice-versa. The example code is still available and I'm sure it could be generalized to C++ quite easily. There are also some other responses in that thread that offer useful advice. At the beginning it is just best to treat R CMD INSTALL as a magical unicorn that gets you where you need to go: http://abstrusegoose.com/120 (keep clicking the images to get the full story) If you are absolutely, positively dying to know what really happens... well, the relative files in the R source are `src/library/tools/R/install.R` and `src/library/tools/R/build.R`. But seriously. Magical unicorn. Takes care of the hard stuff so you can build awesome packages. Hope this helps! -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/FW-Rcpp-devel-Question-on-5-6-Interfacing-C-code-tp3465257p3468640.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
Re: [Rd] FW: [Rcpp-devel] Question on 5.6 Interfacing C++ code
smcguffee wrote: You are right, I looked and I did find the R source code. However, it's largely written in R! I mean, I don't know how to trace the R code where INSTALL is recognized and follow it to a c or c++ level command. For example these are hits in .R files, not c files, and I don't know how to connect ... If you could point me to the functions that are called a c or c++ level, I'd love to see what R is doing for myself. Thanks! Sean Hi Sean! Along with many other people in this thread, I would strongly recommend a top-down approach to this. Build a package, stick some stuff in the src folder, run R CMD INSTALL on it and see what happens. The reason I recommend this approach is that it lets you focus on writing a package that does something useful rather than the nuts and bolts of cross platform compilation and installation. R CMD INSTALL takes care of this for you automagically and it is very good at what it does. I wrote a post some time back about building an example package from scratch that contains C code: http://r.789695.n4.nabble.com/Writing-own-simulation-function-in-C-td1580190.html#a1580423 It begins with the using the package.skeleton() function to kickstart things, discusses how to make sure the compiled code is dynamically loaded when a user runs library(your_package) and even discusses how to call R functions from inside of C functions and vice-versa. The example code is still available and I'm sure it could be generalized to C++ quite easily. There are also some other responses in that thread that offer useful advice. At the beginning it is just best to treat R CMD INSTALL as a magical unicorn that gets you where you need to go: http://abstrusegoose.com/120 (keep clicking the images to get the full story) If you are absolutely, positively dying to know what really happens... well, the relative files in the R source are `src/library/tools/R/install.R` and `src/library/tools/R/build.R`. But seriously. Magical unicorn. Takes care of the hard stuff so you can build awesome packages. Hope this helps! -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/FW-Rcpp-devel-Question-on-5-6-Interfacing-C-code-tp3465257p3467221.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
Re: [Rd] How to get R to compile with PNG support
Dear R devel list, Good morning; I'm with the Sage (http://www.sagemath.org) project. (Some of you might have seen my talk on this at last summer's useR conference). Thanks for stoping by Karl! I have to say that I am a big fan of the Sage project---it is a very good idea and I really appreciate all the time you guys put into it. I may not be able to answer all of your questions concerning PNG support, but hopefully some of the following pointers will be useful. Karl-Dieter Crisman wrote: We have some rudimentary support for using R graphics in various cases, which has proved useful to many of our users who want to go back and forth between R and other capabilities within Sage. Unfortunately, the way we originally implemented this was using the png and plot functions in R itself, which perhaps isn't the best (i.e., everyone uses ggplot now? but I digress). One important distinction to make is between R graphics functions such as plot and ggplot, and R graphics *devices*, such as png. The devices provide back ends that take the R-level function calls and actually execute the low-level draw line from a to b, clip to rectangle A, insert left-justified text at x,y primitives that get written to an output format. Bottom line for Sage is that as long as you implement at least one device function, such as png, your users should be able to call plot, ggplot, and the rest of R's graphics functions to their heart's content, they just won't have a wide selection of output formats. Karl-Dieter Crisman wrote: That means that when people download a binary of ours, or compile their own, whether R's plot and png functions work depends heavily on the rather obscure (to users) issue of exactly what headers are present on the compiling machine. Unfortunately, it is *very* unclear what actually needs to be present! There are innumerable places where this has come up for us, but http://trac.sagemath.org/sage_trac/ticket/8868 and http://ask.sagemath.org/question/192/compiling-r-with-png-support are two of the current places where people have compiled information. The FAQ says, Unless you do not want to view graphs on-screen you need ‘X11’ installed, including its headers and client libraries. For recent Fedora distributions it means (at least) ‘libX11’, ‘libX11-devel’, ‘libXt’ and ‘libXt-devel’. On Debian we recommend the meta-package ‘xorg-dev’. If you really do not want these you will need to explicitly configure R without X11, using --with-x=no. Well, we don't actually need to view graphs on-screen, but we do need to be able to generate them and save them (as pngs, for instance) to the correct directory in Sage for viewing. But we have people who've tried to do this in Ubuntu, with libpng and xorg-dev installed, and the file /usr/include/X11/Xwindows.h exists, but all to no avail. There are almost as many solutions people have found as there are computers out there, it seems - slight hyperbole, but that's what it feels like. We've posted more than once (I think) to the r-help list, but have gotten no useful feedback. Is there *anywhere* that the *exact* requirements R has for having capabilities(png) png FALSE come out TRUE are documented? Then, not only could we be smarter in how we compile R (currently somewhat naively searching for /usr/include/X11/Xwindows.h to determine whether we'll try for png support), but we would be able to tell users something very precise to do (e.g., apt-get foo) if they currently have R without PNG support in Sage. Again, I emphasize that apparently getting xorg-dev doesn't always do the trick. We do realize that for most people wanting to use just R, it's best to download a binary, which will behave nicely; Sage's batteries included philosophy means that we are asking for more specialized info from upstream, and for that I apologize in advance. I also apologize if I said something silly above, because I don't actually know what all these files are - I've just looked into enough support requests to have a decent idea of what's required.We are trying not to have to parse the makefile to figure all this out, and possibly making some mistake there as well. Thank you SO much for any help with this, Karl-Dieter Crisman for the Sage team In the trac ticket you linked, the configure output shows PNG is enabled (I.E. the library was found) but you may be ending up with no support for an actual png() graphics device due to one of the following - configure didn't find Xlib as X11 is not listed under Interfaces - configure didn't find cairo as it is not listed under Additional capabilities So, although R has the PNG library that is only useful for writing PNG files. R also needs the Xlib or Cairo libraries to provide drawing primitives that will create the figures those files will contain. In the ask.sagemath question the problem appears to be that the user had X11 installed but not libpng. I
Re: [Rd] Sweave support added to rgl package
Duncan Murdoch-2 wrote: I have just committed some code to the rgl package on https://r-forge.r-project.org/projects/rgl/ to allow rgl images to be inserted into Sweave documents. (This is not in the CRAN version yet.) It makes use of the custom graphics driver support added by Brian Ripley. In R-devel (which will become R 2.14.0 next spring in New Zealand, next fall in most other places), usage is quite straightforward. For example, code like this in a Sweave document: lt;fig=true, grdevice=rgl.Sweave, pdf=false, stayopen=TRUEgt;= x - rnorm(100); y - rnorm(100); z - rnorm(100) plot3d(x, y, z) @ will insert a .png snapshot of the figure. Because that chunk has stayopen=TRUE, it can be followed by another chunk to add to the figure, e.g. lt;fig=true, grdevice=rgl.Sweave, pdf=falsegt;= lines3d(x[1:10], y[1:10], z[1:10], col=red) @ All of this is possible in R 2.13.0, but it takes more work: see the ?rgl.Sweave help page. I will eventually add postscript and PDF output options as well, and perhaps some support for the LaTeX movie15 package, but those are not there yet. Comments or bug reports are welcome. Duncan Murdoch This is great news Duncan! If you do consider adding support for movie15, the Asymptote graphics language may be handy: http://asymptote.sourceforge.net/ Asymptote can embed 3D graphs into LaTeX documents that are fully zoomable/manipulatable. It also uses LaTeX to typeset the figure text. -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/Sweave-support-added-to-rgl-package-tp3461163p3463653.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
Re: [Rd] Patching update.packages to enable updating of only a user defined subset of packages
Tal Galili wrote: Hello dear R developers, I recently found out that it is not possible to limit update.packages() to update only a few packages at a time. The patch offered simply adds a 'subset' parameter and the statement bounded within if(!missing(subset)) to implement it. The code is pasted bellow (and also attached as an .r file). Might this patch be considered valuable to be added to R? (in the code bellow I called the function update.packages.2 so to not mask the original update.packages) With much respect, Tal Hi Tal, I think if you pass a character vector in the `oldPkgs` argument of update.packages, it will only consider packages in that list for updating. -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/Patching-update-packages-to-enable-updating-of-only-a-user-defined-subset-of-packages-tp3456738p3463670.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
[Rd] R 2.13.0-beta for Windows, file.copy() throws suspicious errors due to default value of copy.mode
While checking packages against R 2.13.0-beta on Windows, I have run into a
few strange error messages related to copying files. The errors all relate
to file.copy() and have the form of:
Error in Sys.chmod(to[okay], file.info(from[okay])$mode, TRUE) :
'mode' must be of length at least one
After half a day of tinkering, the best reproducible example I can come up
with involves using Roxygen to generate man files for the tikzDevice:
# Install roxygen from CRAN and grab tikzDevice source code
R --vanilla --slave -e install.packages('roxygen')
git clone git://github.com/Sharpie/RTikZDevice.git
# Generate documentation, first run succeeds:
R --vanilla --slave -e require(roxygen); roxygenize('RTikZDevice',
'RTikZDevice.build', overwrite = TRUE)
Loading required package: roxygen
Loading required package: digest
Writing anyMultibyteUTF8Characters to
RTikZDevice.copy/man/anyMultibyteUTF8Characters.Rd
Warning in parse.name(partitum) :
No name found for the following expression in RTikZDevice/R/cacheMetrics.R
line 3:
`NULL . . .'
Writing queryMetricsDictionary to
RTikZDevice.copy/man/queryMetricsDictionary.Rd
...
Writing namespace directives to RTikZDevice.copy/NAMESPACE
Merging collate directive with RTikZDevice/DESCRIPTION to
RTikZDevice.copy/DESCRIPTION
# Try running it again, and it bombs:
R --vanilla --slave -e require(roxygen); roxygenize('RTikZDevice',
'RTikZDevice.build', overwrite = TRUE)
Loading required package: roxygen
Loading required package: digest
Error in Sys.chmod(to[okay], file.info(from[okay])$mode, TRUE) :
'mode' must be of length at least one
Calls: roxygenize - copy.dir - file.copy - Sys.chmod
In addition: Warning message:
In file.create(to[okay]) :
cannot create file
'RTikZDevice.copy/.git/objects/pack/pack-cc0dd1e2622e87f86f8c5a8e617fbf77e253cea1.idx',
reason 'Permission denied'
Execution halted
If I replace all calls to file.copy(...) in the roxygen package with
file.copy(..., copy.mode = FALSE) and reinstall it, then I can regenerate
package documentation all day long without errors. I also get no errors when
I perform the same task with R 2.12.2 on Windows or R 2.13.0-beta on OS X
and Linux.
Maybe roxygenize() is abusing file.copy() somehow, but I find the 'mode'
must be of length at least one error suspicious.
Any ideas?
Using:
Windows 7 x86_64
R 2.13.0-beta
Rtools 2.13
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
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Re: [Rd] embed Sweave driver in .Rnw file
Friedrich Leisch wrote:
On Tue, 14 Dec 2010 12:40:04 +0100,
Romain Francois (RF) wrote:
Hello,
Sweave lets you use alternative drivers through the driver argument,
and
several packages take advantage of that and define custom Sweave
driver
for various purposes. Most of them are listed on the Reproducible
Research CTV:
(http://cran.r-project.org/web/views/ReproducibleResearch.html)
The next natural step is for package developpers to take advantage of
this in their vignettes. In Rcpp we work around the way package
building
works and we do:
- let R build a dummy vignette
- then use the inst/doc/Makefile to replace it with a vignette that is
processed by the driver from the highlight package (giving syntax
highlighting).
I played with Sweave so that it would be able to create the driver
from
some text included in the text of the .Rnw file:
$ svn diff
Index: src/library/utils/R/Sweave.R
===
--- src/library/utils/R/Sweave.R (revision 53846)
+++ src/library/utils/R/Sweave.R (working copy)
@@ -20,6 +20,16 @@
# We don't need srclines for code, but we do need it for text, and
it's easiest
# to just keep it for everything.
+SweaveGetDriver - function(file){
+txt - readLines(file)
+line - grep( \\SweaveDriver, txt, value = TRUE )
+if( length(line) ){
+txt - sub( ^.*\\SweaveDriver[{](.*)[}], \\1, line[1L] )
+driver - try( eval( parse( text = txt ) ), silent = TRUE )
+if( !inherits( driver, try-error) ) driver
+}
+}
+
Sweave - function(file, driver=RweaveLatex(),
syntax=getOption(SweaveSyntax), ...)
{
@@ -28,7 +38,9 @@
else if(is.function(driver))
driver - driver()
-
+drv - SweaveGetDriver(file)
+if( !is.null(drv) ) driver - drv
+
if(is.null(syntax))
syntax - SweaveGetSyntax(file)
if(is.character(syntax))
This allows one to write something like this in their file:
%\SweaveDriver{ { require(highlight); HighlightWeaveLatex() } }
So that when calling :
Sweave( somefile.Rnw )
the highlight driver is used instead of the default driver.
Could something like that be added to Sweave ?
Yes, sure!
Will have a look at the patch later this week and apply it if it
passes the tests. The patch is against a current r-devel?
Best,
Fritz
Is there an update on the status of this patch? I use a particularly ugly
hack to splice a custom driver into one of my package Vignettes and it would
be great to retire it in favor of an officially supported method.
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
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Re: [Rd] Incorrect positioning of raster images on Windows
Michael Sumner-2 wrote:
I think there's something about the discrete cell versus centre value
interpretation here, and you are pushing the pixels through R's graphics
engine as well as whatever the png device has to do.
I can't enlighten you about the details of that, but by creating an image
file more directly with pixels as data you can get the result exactly:
test - matrix(c(0, 255), 3, 5)
library(rgdal)
## transpose to get orientation right
x - image2Grid(list(x = 1:ncol(test), y = 1:nrow(test), z = t(test)))
writeGDAL(x, raster.png, driver = PNG, type = Byte)
On Mon, Oct 18, 2010 at 3:17 PM, Sharpie ch...@sharpsteen.net wrote:
I am working on dumping raster data from R into PNG files using
rasterImage(). I am working with a test matrix from the rasterImage()
example and using it to produce a PNG image with the following code:
# From the example for rasterImage(). A 3 pixel by 5 pixel b/w
checkerboard.
testImage - as.raster(0:1, nrow=3, ncol=5)
testImage
[,1] [,2] [,3] [,4] [,5]
[1,] #00 #FF #00 #FF #00
[2,] #FF #00 #FF #00 #FF
[3,] #00 #FF #00 #FF #00
png('test.png', width=5, height=3, units='px')
# Just want the image, no margins, boarders or other fancy stuff.
par(mar = c(0,0,0,0) )
plot.new()
plotArea = par('fig')
rasterImage(testImage, plotArea[1], plotArea[3],
plotArea[2], plotArea[4], interpolate = FALSE )
dev.off()
However, using R 2.12.0, 64 bit on Windows 7 I have a strange issue where
the image is shifted up by one row and to the left by one row. In other
words, the bottom row of pixels is missing along with the right column.
The
code works as I expect it to on OS X and Debian.
Am I misusing the plotting commands in some way or should I submit an
off-by-one bugreport to Bugzilla?
Any suggestions or comments are most welcome.
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Michael Sumner
Institute for Marine and Antarctic Studies, University of Tasmania
Hobart, Australia
e-mail: mdsum...@gmail.com
Hi Micheal,
I appreciate the suggestion. However, rgdal is very heavyweight and
installing the GDAL library is not a trivial operation automagically handled
`install.packages()` on every platform R supports. As I am not doing
spatial analysis, I am very reluctant to add rgdal to the dependency list of
my package.
I would very much prefer to find the root cause of the difference in `png()`
behavior on Windows when compared to OS X and Linux. If anyone on this list
has some insight to share, I would be very grateful to hear it.
I waffled a bit on whether to send this to R-help or R-devel, in the light
of day (as opposed to the foggy darkness that surrounds 2am) think it may be
more of an R-devel question. Forwarding it there now.
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
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Re: [Rd] How do you make a formal feature request?
Donald Paul Winston wrote: Who decides what features are in R and how they are implemented? If there is someone here who has that authority I have this request: A report() function analogous to the plot() function that makes it easy to generate a report from a table of data. This should not be in some auxiliary package, but part of the core R just like plot(). As a long time SAS user I cannot believe R does not have this. Please don't give me any crap about Sweave, LaTex, and the power of R to roll your own. You don't have to roll your own plot do you? Reports are no different. If you don't agree do not bother me. If you agree then please bring this request to the appropriate authorities for consideration or tell me how to do it. Well, I can think of three ways it can go down: 1. You want a shiny new pony. You ask about it on the mailing list and it seems that everyone else in the world responds Hell yeah! I want to ride that too!. In this case the natives are restless enough that someone on R-Core may personally implement the feature- especially if they want to ride the pony as well. In this case, you need to provide a detailed specification of what kind of pony you want, how it should be groomed and the exact pitch at which you want it to whinny. A good template for such as spec would be a Python Enhancement Proposal (PEP) which is the way community-suggested core changes are implemented in python. An example is: http://www.python.org/dev/peps/pep-0389/ However, going this route is extremely rare. You have to have a significant amount of the user community rallying behind your idea and buy-in from core developers who are interested in implementing and, most importantly, maintaining and supporting the code. 2. You want a shiny new pony but not many other people in the word seem interested. In this situation you can do the work yourself, or with a group of other like-minded pony enthusiasts, to bring your idea into the world. Perhaps the genetic material you are looking for is already present in the vast herds of other ponies running wild on CRAN and elsewhere and you just have to do a little breeding to get what you want. Other times, the only way to do right is to write everything from scratch. Either way, in the end you will have a pony that shines exactly the way you want it to that you can enjoy for the rest of your life. In this case, getting your new pony into R Core is unlikely. The best response you can hope for is something along the lines of That is a mighty fine pony you have there, but we really don't want it crapping all over our stable. They are not trying to be rude- the facts of life are that the members of R Core have a limited amount of time and a lot of other ponies to clean up after. Add to that the fact that shoveling pony shit is a thankless job that does not pay well and it is understandable why R Core may be conservative about the number of ponies they let into the official stable. However, they will be more than happy to provide your pony with a stall at CRAN so that everyone else in the world can take it out for a spin. I have never had a problem with installing and using packages from CRAN, even on windows machines that have been locked down and then shot in both kneecaps by the friendly neighborhood IT gestapo. All and all, this option is actually a pretty sweet deal; you will just have to drop by the CRAN stall every once and a while and deal with the pony droppings yourself or people will start to avoid it because of the smell. 3. You want a shiny new pony, but dont have the time or energy to pick out or put together the exact one you want. In this case, you can still get the pony you want but it will cost you money. There are R programmers out there who can write you a package if you pay them the right price. Supporting your local grad student population can also work; hunger is a great motivator. In the end you can also pay a corporate pony breeder like SAS for a trusty thoroughbred that is well respected by people in high places. However, you may notice that these ponies bear some telltale signs of inbreeding-- one of their eyes may not point in the same direction as the other or the pony becomes confused easily when put in an unfamiliar situation. Given there is not a lot you can do about these defects, you may suffer a crippling case of buyers remorse especially when you see the bill. Ok, I think i've thoroughly beat this horse analogy to death and I'm going to stop now. -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/How-do-you-make-a-formal-feature-request-tp2333593p2333737.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
Re: [Rd] C or Java code generation
Romain Francois wrote: Hi, It installs just like any other R package, there is no need for a Makefile. $ R CMD RInside_0.2.3.tar.gz Should probably be: R CMD INSTALL RInside_0.2.3.tar.gz But are we misleading the OP a little bit about what RInside can help him do? His original question was: Vyacheslav Karamov wrote: Hi All! I'm new to R and I need to know is it possible for R to generate C/C++ source code, Java byte code or native Win32 DLL like MatLab? He stated that he was looking for this because: Vyacheslav Karamov wrote: Is there any posibility to use R without installing? I mean that I have my own application written in MS Visual C++ and I need to use R script in this app. I can install R and use it via DCOM, but it's not convenient for the end users of my program. I think the proper answer to this question is: R is an interpreted language. There is not any developed way to compile R code to machine code, an executable or a library that can be distributed to a computer that does not have a copy of R installed. R does include a library with various names such as R.a, libR.so and R.dll that contains the R interpreter and support functions which could be used to distribute a stand alone executable that can run R code without the R distribution being installed. However the sticking point is packages; the OP is likely trying to embed R in order to gain access to one, or several, R packages. As far as I know, there is no developed way to compile an R package down such that it could be distributed, perhaps along with R.dll, and stand by its self. It is theoretically possible, but there is no turnkey solution. So, unless I am gravely mistaken, RInside is just a nice cross-platform replacement for the RDCOM interface. It won't solve the problem of needing R installed on the client's computer in order to fully use the R environment which is dependent on packages. -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/C-or-Java-code-generation-tp2330875p2332606.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
Re: [Rd] C or Java code generation
Dirk Eddelbuettel wrote: On 20 August 2010 at 08:02, Sharpie wrote: | So, unless I am gravely mistaken, RInside is just a nice cross-platform | replacement for the RDCOM interface. It won't solve the problem of needing I wrote RInside, and I am unaware of any attempts of mine to either copy, clone or otherwise imitate any of the non-portable technologies from the Pacific Northwest I happen to be rather unfamiliar with to boot. So I fear that were indeed gravely mistaken. Thanks for trying though. RInside delivers what it promises: an embedded R instance for your C++ program. And thanks to the magic that is Rcpp and all of the work Romain and I put into it, you get a rather rich interface between R and C++ that has no parallel I know of. | R installed on the client's computer in order to fully use the R environment | which is dependent on packages. That on the other hand is a true statement and as far as I am concerned a good thing as well. Dirk My apologies Dirk, I phrased that badly. What I ment is that RInside provides an interface by which the C++ program can interact with R. Essentially, what the OP would gain from RInside is that he would not have to use DCOM. -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/C-or-Java-code-generation-tp2330875p2332632.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
[Rd] Rserve graphics output [was Re: C or Java code generation]
Donald Paul Winston wrote: Aren't you the guy who created Rserve? I'd like to develop a web app so clients can perform exploratory data analysis with their browser with no installed software, not even java (I don't like applets). I thought R would be excellent for this but I need some issues cleared up before I invest a lot of time working with it. Well, Simon is the one who create Rserve. However, if you have questions about Rserve it may be best to start a new thread or at least change the subject header of your message. This discussion was about creating stand-alone executables that use R code for deployment on a desktop. Donald Paul Winston wrote: It appears R insists on directing plot output to a file. Is their a graphics device that keeps the output in memory so it can be returned to my java app as a stream of bytes? If I have to wait for it to write to a unique file and then read it back again then I don't think that's going to work. My web app needs to support hundreds of concurrent clients. As far as I know all R graphics output that does not go to a screen device, such as an X window, must be directed to some sort of file. I am not aware of a graphics device that provides output to something other than a screen or a file, but there very well may be such a device in existence. The functionality you could describe could be implemented by writing a R graphics device that forwards the R plotting commands to... well anywhere you want, really. As the author of an R graphics device, I can say the trickiest part of such an undertaking will be calculating font metrics so that R can properly position text in the graphics. Everything else is very straight-forward. I have plans to write a device that forwards the plotting commands to a socket connection that allows another program to execute them. In my case, an Erlang backbone is used to route the results back to web clients using websockets. The idea is to have the plot rendered directly in the client's browser using a JavaScript library like RaphealJS. However, the school year is upon me and the project will probably remain on the drawing board until next summer. Donald Paul Winston wrote: Is REngine.jar and REngineRserve.jar all I need in my web app? I can't comment on REngine as I have not used it. Donald Paul Winston wrote: Also, how come their is no shutdown command from the command line for Rserve. I see one in the java client api. Do I have to write my own? I find that on UNIX a SIGTERM, SIGSTOP or SIGKILL signal broadcast using a command line utility such as kill does the job. -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/C-or-Java-code-generation-tp2330875p2332761.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
Re: [Rd] [R] Use of .Fortran
Prof Brian Ripley wrote:
Well, it is not Fortran 77 but Fortran 95, and so needs to be given a
.f95 extension to be sure to work.
I think most compilers only distinguish two fortran file extensions: .f or
.f90. .f denotes fixed-form source code while .f90 denotes free-form. Some
compilers also take the capitalized versions, .F and .F90, to indicate
source code that must be run through a preprocessor.
It is a little weird, but Fortran file extensions have nothing to do with
the year of the language standard the code is to be compiled against.
David Scott wrote:
file SSFcoef.f
subroutine SSFcoef(nmax,nu,A,nrowA,ncolA)
implicit double precision(a-h,o-z)
implicit integer (i-n)
integer l,i,nmax
double precision nu,A(0:nmax,0:nmax)
A(0,0) = 1D0
do l=1,nmax
do i=1,l-1
A(l,i) = (-nu+i+l-1D0)*A(l-1,i)+A(l-1,i-1)
end do
A(l,0) = (-nu+l-1D0)*A(l-1,0)
A(l,l) = 1D0
end do
return
end
I created a dll (this is windows) using R CMD SHLIB SSFcoef.f
Then my R code is:
### Load the compiled shared library in.
dyn.load(SSFcoef.dll)
### Write a function that calls the Fortran subroutine
SSFcoef - function(nmax, nu){
.Fortran(SSFcoef,
as.integer(nmax),
as.integer(nu)
)$A
}
SSFcoef(10,2)
which when run gives
SSFcoef(10,2)
NULL
I am pretty sure the problem is that I am not dealing with the matrix A
properly. I also tried this on linux and got a segfault.
Can anyone supply the appropriate modification to my call (and possibly to
the subroutine) to make this work?
When calling a Fortran function for R, for each argument that appears in the
subroutine declaration:
subroutine subName(...arg list...)
You *must* provide a matching input to the .Fortran() call:
.Fortran(subName, ...arg list...)
In the case of arrays that are filled by the Fortran subroutine, just pass
an empty vector of the appropriate length- perhaps created using the
double() function.
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
--
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[Rd] Rtools for building 64 bit windows packages
Hello R developers, I sincerely apologize if the answer to this question is clearly documented somewhere, but I was unable to figure it out over my morning coffee. I just downloaded today's release of R 2.11.0 and installed it on my Windows 7 64 bit VM. I also downloaded the latest version of Rtools211 from Professor Murdoch's site. The first thing I attempted to do was build some of my packages from source to check that they work with the new version. I got the following error message: making DLL ... x86_64-w64-mingw32-gcc -IC:/PROGRA~1/R/R-211~1.0-X/include -O2 -Wall -std=gnu99 -c tikzDevice.c -o tikzDevice.o x86_64-w64-mingw32-gcc: not found This does not surprise me, R 2.11.0 is hot out of the forge and Rtools probably hasn't been repacked to support the 64 bit version. I gathered from the Windows FAQ and the list archives that the MinGW-w64 project supplies the compilers and linkers used by the 64 bit version- I visited their site and found the selection of packages available for download... confusing. I guess what I'm asking: * Do I use the Cygwin binaries? * If not, is there an officially blessed binary distribution of Windows x86_64 compilers and binutils? * If not, do I build the x86_64 toolchain from the current HEAD, or is there a specific revision that has been determined to be stable? Thanks for your time and effort on maintaining and enhancing such a wonderful language! -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/Rtools-for-building-64-bit-windows-packages-tp2021034p2021034.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
Re: [Rd] Rtools for building 64 bit windows packages
Duncan Murdoch-2 wrote: You can use the Rtools for the stuff other than the compilers. You need the MinGW 64 bit versions of the compilers; they are not nicely packaged yet, but the instructions for finding them are in the new version of the R-admin manual, in the section 3.3, Building R for 64 bit Windows. Ahh, thank you Duncan- this was exactly the information I was looking for. When I looked in R-admin this morning, I skipped straight to Appendix D as I wasn't interested in building R, just packages. Thanks again! -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://r.789695.n4.nabble.com/Rtools-for-building-64-bit-windows-packages-tp2021034p2022510.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
Re: [Rd] .Fortran interface error
jgarcia-2 wrote: Yes That's it! Thanks a lot!! Changing UNIT=5 in the F95 code by UNIT=7 solves the collision. Thank you very much Charlie, I've spent a lot of hours with this. I'm glad it worked! Google seems to indicate that units 0, 5, 6, 100, 101 and 102 are special in Fortran. However, the professor who taught me Fortran recommended using unit numbers that were 11 or greater as his experience with several Fortran compilers was that they tended to appropriate units = 10 for their own uses and this behavior was not well standardized. I haven't been able to verify this myself, but there may be something to his warning. jgarcia-2 wrote: Still R -d valgrind --vanilla foofortran.Rcheck/foofortran-Ex.R gives 3 errors (two Invalid read of size 8 and one Syscall param write(buf) points to uninitialised byte(s)), which are the same it gave with UNIT=5. However, everything seems to work fine now in the normal execution :-) Thank you very much again Javier I'm not well acquainted with valgrind so I can't offer any advice on this part :( Good luck! -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://n4.nabble.com/Fortran-interface-error-tp1838225p1839012.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
Re: [Rd] SHLIB works but inline compilation does not
Jeff Brown wrote:
Hi,
I appear to be able to compile, load and call shared objects using SHLIB
and .Call:
code - '#include R.h\n #include Rdefines.h\n SEXP f(){\n return
R_NilValue ; }'
writeLines( code, test.c )
system( R CMD SHLIB test.c )
gcc -arch i386 -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386
-I/usr/local/include-fPIC -g -O2 -c test.c -o test.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
-mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module
-multiply_defined suppress -L/usr/local/lib -o test.so test.o
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
dyn.load( test.so )
.Call( f )
NULL
The above follows Romaine-Francois 3's suggestion here:
http://n4.nabble.com/I-can-t-run-the-example-shown-in-the-inline-package-td1774328.html#a1778838
However, when I try to use the inline package, I can't get it to work:
code -
+ int i, j, nab = *na + *nb - 1;
+ for(i = 0; i nab; i++)
+ ab[i] = 0.0;
+ for(i = 0; i *na; i++) {
+ for(j = 0; j *nb; j++)
+ ab[i + j] += a[i] * b[j];
+ }
fun - cfunction(
+ signature(a=numeric, na=numeric, b=numeric, nb=numeric,
ab=numeric),
+ code,
+ language=C,
+ convention=.C )
ERROR(s) during compilation: source code errors or compiler configuration
errors!
Program source:
1: #include R.h
2:
3:
4: void file4431b782 ( double * a, double * na, double * b, double * nb,
double * ab ) {
5:
6: int i, j, nab = *na + *nb - 1;
7: for(i = 0; i nab; i++)
8:ab[i] = 0.0;
9: for(i = 0; i *na; i++) {
10:for(j = 0; j *nb; j++)
11:ab[i + j] += a[i] * b[j];
12: }
13: }
Error in compileCode(f, code, language, verbose) :
Compilation ERROR, function(s)/method(s) not created!
The C function above is the one from Writing R Extensions, p. 79; the
suggestion for how to compile it inline is from Dirk Eddelbuettel, at this
thread:
http://n4.nabble.com/Getting-started-with-C-td1837912.html#a1837912
R says it's either a source code or configuration error. I got the code
from Writing R Extensions, and Dirk tried it out too. But if it's a
compilation error, then shouldn't the first method (with SHLIB) not work
either?
I realize I could stick to the SHLIB method, which Charlie (The Sharpie)
Sharpsteen wrote up in fantastic detail here:
http://n4.nabble.com/Writing-own-simulation-function-in-C-td1580190.html#a1580423
But there's so much more stuff I'll need to understand if I do it that way
...
I use an Intel MacBook Pro with OS X 10.6.2, XCode 3.2.1, gcc 4.2.1.
Thanks,
Jeff
I could not reproduce this problem on my computer, OS X 10.6.3, gcc 4.2.1, R
2.10.1, inline 0.3.4:
code -
int i, j, nab = *na + *nb - 1;
for(i = 0; i nab; i++)
ab[i] = 0.0;
for(i = 0; i *na; i++) {
for(j = 0; j *nb; j++)
ab[i + j] += a[i] * b[j];
}
fun - cfunction(
signature(a=numeric, na=numeric, b=numeric, nb=numeric,
ab=numeric),
code,
language=C,
convention=.C )
fun( 1:3, 3, 4:6, 3, double(5) )
$a
[1] 1 2 3
$na
[1] 3
$b
[1] 4 5 6
$nb
[1] 3
$ab
[1] 4 13 28 27 18
The only thing I can think of is that you may have a newline issue going on.
Here's the dump of the code object:
dput(code)
\nint i, j, nab = *na + *nb - 1; \nfor(i = 0; i nab; i++) \n ab[i] =
0.0; \nfor(i = 0; i *na; i++) { \n for(j = 0; j *nb; j++) \n ab[i + j]
+= a[i] * b[j]; \n}
Do you have newlines, \n, that are in different places? An easy way to
check may be to copy the results of running dput() on your code object into
one file, mine into another and running diff.
Hope this helps!
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
--
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Re: [Rd] Getting started with .C
Jeff Brown wrote:
Hi,
I'm trying to learn to use .C, which lets one invoke compiled C code from
within R. To do that, one has to first get the C code into R as a shared
object, which (I think) means first compiling it (with COMPILE or SHLIB)
and then loading it (with dyn.load()).
I would suggest taking it a step further and building an R package to hold
your compiled code. The pros are:
* It keeps the R wrapper scripts and other things you will end up
creating packaged together with your code.
* It handles compilation automagically during installation.
* It handles loading the dylib for you.
The only con I can think of is:
* It takes ~2 extra minutes of your time to set up. But compared to
other languages I have used this is a ridiculously small price to pay for
the portability and organization offered by packages.
I wrote a post that goes through step-by-step how to do this for the .Call()
interface, including example code. You can find it at:
http://n4.nabble.com/Writing-own-simulation-function-in-C-td1580190.html#a1580423
In Writing R Extensions, p. 79, they give the following example of a C
program for convolution of two vectors. (The details aren't important; it's
just a function that does something to some stuff.)
void convolve (double *a, int *na, double *b, int *nb, double *ab) {
int i, j, nab = *na + *nb - 1;
for(i = 0; i nab; i++)
ab[i] = 0.0;
for(i = 0; i *na; i++)
for(j = 0; j *nb; j++)
ab[i + j] += a[i] * b[j]
}
Jeff Brown wrote:
The document suggests calling it from R like this (again the details
aren't important):
conv - function(a, b)
.C(convolve,
as.double(a),
as.integer(length(a)),
as.double(b),
as.integer(length(b)),
ab = double(length(a) + length(b) - 1))$ab
I wrote a file, convolve.c, with nothing but the above C code in it. I
can't figure out how to compile it. I don't understand the syntax (no
parentheses?) and I always get the same information-free error message:
list.files()
[1] AERconvolve.c sendmailR
R CMD SHLIB compile.c
Error: syntax error
COMPILE compile.c
Error: syntax error
R CMD SHLIB compile
Error: syntax error
COMPILE compile
Error: syntax error
R CMD SHLIB compile.c
Error: syntax error
COMPILE compile.c
Error: syntax error
R CMD SHLIB compile
Error: syntax error
COMPILE compile
Error: syntax error
I'm using an Intel MacBook Pro running Leopard. At a console, typing gcc
--version yields 4.2.1. I know I'm supposed to be using version 4.2; I
thought 4.2.1 would qualify, but please let me know if I'm wrong about
that.
For guidance I've been relying on Writing R Extensions, R Installatino
and Administration, the R for Mac OS X Developer's Page, and the
built-in help. Please let me know if there are other important resources
I've missed.
Many thanks,
Jeff
All R CMD commands must be executed at the command line- i.e. in a Windows
CMD shell or Unix/Linux bash shell. They are not meant for use inside the R
interpreter.
Hope this helps!
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
--
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Re: [Rd] Tabs in R source code
pengyu.ut wrote: http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html Here is the R style, which does not recommend using tabs. Although it might take some time to forbidden the use of tabs, it will eventually be a good practice that benefits everyone in the future. Whoa, put the kibosh on that thought. That is Google's style guide for R code written at Google by Google employees. It is by no means the style guide adopted by the R core team. Representing it as the official R style guide is just inviting a torrent of flaming email. -- View this message in context: http://n4.nabble.com/Tabs-in-R-source-code-tp930751p948240.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
