[Rd] useDynLib in older versions e.g. (2.10)
Hi, Has something changed regarding the useDynLib in the NAMESPACE file in packages? I've written a package that works in e.g. 2.12/2.13 but simply cannot find the dynamic library under windows. The version on CRAN is older than the one I'm talking about and depends on a newer version of R but I want to make the package available to people with older versions. > utils:::menuInstallLocal() package 'lassoshooting' successfully unpacked and MD5 sums checked > require(lassoshooting) Loading required package: lassoshooting Error in library.dynam(lib, package, package.lib) : shared library 'lassoshooting' not found In addition: Warning message: package 'lassoshooting' was built under R version 2.13.0 I'm usually under linux and don't know about the gory details of .dll files. NAMESPACE file -- useDynLib(lassoshooting) export(lassoshooting) happy easter! regards, Tobias -- Tobias Abenius Ph.D. Student, M.Sc. in Computer Science Mathematical Statistics Mathematical Sciences University of Gothenburg * installing *source* package 'lassoshooting' ... ** libs *** arch - i386 gcc -I"D:/RCompile/recent/R-2.13.0/include" -I"d:/Rcompile/CRANpkg/extralibs/local/include" -O3 -Wall -std=gnu99 -c ccd_common.c -o ccd_common.o ccd_common.c: In function 'ccd_common': ccd_common.c:118:2: warning: #warning Using R fortran BLAS calls gcc -I"D:/RCompile/recent/R-2.13.0/include" -I"d:/Rcompile/CRANpkg/extralibs/local/include" -O3 -Wall -std=gnu99 -c ccd_r.c -o ccd_r.o ccd_r.c: In function 'ccd': ccd_r.c:163:5: warning: too many arguments for format ccd_r.c:156:7: warning: unused variable 'ret' ccd_r.c:18:11: warning: 'X' may be used uninitialized in this function ccd_r.c:18:14: warning: 'y' may be used uninitialized in this function gcc -shared -s -static-libgcc -o lassoshooting.dll tmp.def ccd_common.o ccd_r.o -Ld:/Rcompile/CRANpkg/extralibs/local/lib -LD:/RCompile/recent/R-2.13.0/bin/i386 -lRblas -lgfortran -LD:/RCompile/recent/R-2.13.0/bin/i386 -lR installing to d:/RCompile/CRANguest/R-release/lib/lassoshooting/libs/i386 *** arch - x64 x86_64-w64-mingw32-gcc -I"D:/RCompile/recent/R-2.13.0/include" -I"d:/Rcompile/CRANpkg/extralibs64new/local/include" -O2 -Wall -std=gnu99 -c ccd_common.c -o ccd_common.o ccd_common.c: In function 'ccd_common': ccd_common.c:118:2: warning: #warning Using R fortran BLAS calls x86_64-w64-mingw32-gcc -I"D:/RCompile/recent/R-2.13.0/include" -I"d:/Rcompile/CRANpkg/extralibs64new/local/include" -O2 -Wall -std=gnu99 -c ccd_r.c -o ccd_r.o ccd_r.c: In function 'ccd': ccd_r.c:163:5: warning: too many arguments for format ccd_r.c:156:7: warning: unused variable 'ret' ccd_r.c:18:11: warning: 'X' may be used uninitialized in this function ccd_r.c:18:14: warning: 'y' may be used uninitialized in this function x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o lassoshooting.dll tmp.def ccd_common.o ccd_r.o -Ld:/Rcompile/CRANpkg/extralibs64new/local/lib -LD:/RCompile/recent/R-2.13.0/bin/x64 -lRblas -lgfortran -LD:/RCompile/recent/R-2.13.0/bin/x64 -lR installing to d:/RCompile/CRANguest/R-release/lib/lassoshooting/libs/x64 ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'lassoshooting' as lassoshooting_0.1.3-6.zip * DONE (lassoshooting) __ 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
Followup with the specific issue in our most recent (non-posted, as of yet) attempts on a certain box. We now have xorg-dev, libcairo-dev, and Xwindows.h and libpng (as below) on this machine, but R is not compiling with support for any of these things. Once again, any help knowing *exactly* what to pass to the configuration script or anything else would be *greatly* appreciated. We are planning to use R in Sage on several occasions with this machine this summer if we can get this going (see http://www.maa.org/prep/2011/sage.html). R is now configured for i686-pc-linux-gnu Source directory: . Installation directory:/home/sageserver/sage/local C compiler:gcc -std=gnu99 -I/home/sageserver/sage/local/include -L/home/sageserver/sage/local/lib/ Fortran 77 compiler: sage_fortran -g -O2 C++ compiler: g++ -g -O2 Fortran 90/95 compiler:sage_fortran -g -O2 Obj-C compiler: Interfaces supported: X11 External libraries:readline, BLAS(ATLAS), LAPACK(generic) Additional capabilities: PNG, NLS Options enabled: shared R library, R profiling Recommended packages: yes However: > capabilities() jpeg png tifftcltk X11 aqua http/ftp sockets FALSEFALSEFALSEFALSEFALSEFALSE TRUE TRUE libxml fifo clediticonv NLS profmemcairo TRUE TRUE TRUE TRUE TRUEFALSEFALSE __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Window binary packages built for R 2.13.0 do not work in 2.10.0 (was useDynLib in older versions e.g. (2.10))
On Wed, 20 Apr 2011, Tobias Abenius wrote: Hi, Has something changed regarding the useDynLib in the NAMESPACE file in packages? No. As the FAQ asked re bug reports, please don't post speculation rather than problem description. I've written a package that works in e.g. 2.12/2.13 but simply cannot find the dynamic library under windows. The version on CRAN is older than the one I'm talking about and depends on a newer version of R but I want to make the package available to people with older versions. Do you mean 'make a binary version of the package '? Binary packages are (on all platforms, but specifically on Windows and Mac OS X) intended for use only on the same 2.x.[012] versions of R. That warning was not meant to be ignored! If you had bothered to read the CHANGES file you would known that the location of files on Windows binary installations changed in R 2.12.0: of course there is no way that R 2.10.0 (as the posting guide points out there is no '2.10') could know that was going to be changed a year later. The solution is for you to prepare a binary package for each version of R you want it available with and make it available on your own repository. utils:::menuInstallLocal() package 'lassoshooting' successfully unpacked and MD5 sums checked require(lassoshooting) Loading required package: lassoshooting Error in library.dynam(lib, package, package.lib) : shared library 'lassoshooting' not found In addition: Warning message: package 'lassoshooting' was built under R version 2.13.0 I'm usually under linux and don't know about the gory details of .dll files. NAMESPACE file -- useDynLib(lassoshooting) export(lassoshooting) happy easter! regards, Tobias -- Tobias Abenius Ph.D. Student, M.Sc. in Computer Science Mathematical Statistics Mathematical Sciences University of Gothenburg -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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
Hi Charlie, thanks for writing back.
Using the oldPkgs parameter wouldn't work, please see the error bellow:
> update.packages(oldPkgs =c("rpart"))
Error in update.packages(oldPkgs = c("rpart")) :
invalid 'oldPkgs'; must be a result from old.packages()
Do you think it should support this instead of adding a "subset" parameter?
Cheers,
Tal
Contact
Details:---
Contact me: tal.gal...@gmail.com | 972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
--
On Wed, Apr 20, 2011 at 8:34 PM, Sharpie wrote:
>
> 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.
>
> __
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Re: [Rd] useDynLib in older versions e.g. (2.10)
On 20.04.2011 13:30, Tobias Abenius wrote: Hi, Has something changed regarding the useDynLib in the NAMESPACE file in packages? I've written a package that works in e.g. 2.12/2.13 but simply cannot find the dynamic library under windows. The version on CRAN is older than the one I'm talking about and depends on a newer version of R but I want to make the package available to people with older versions. > utils:::menuInstallLocal() package 'lassoshooting' successfully unpacked and MD5 sums checked > require(lassoshooting) Loading required package: lassoshooting Error in library.dynam(lib, package, package.lib) : shared library 'lassoshooting' not found In addition: Warning message: package 'lassoshooting' was built under R version 2.13.0 Yes, your package was built doe R-2.13.0 but you are using R <= 2.12.0 where the dll files were located in a different directory. Hence a) time to upgrade your R version or b) Install the package from sources yourself for the (unstated) version of R on your Windows machine. Uwe Ligges I'm usually under linux and don't know about the gory details of .dll files. NAMESPACE file -- useDynLib(lassoshooting) export(lassoshooting) happy easter! regards, Tobias 00install.out * installing *source* package 'lassoshooting' ... ** libs *** arch - i386 gcc -I"D:/RCompile/recent/R-2.13.0/include" -I"d:/Rcompile/CRANpkg/extralibs/local/include" -O3 -Wall -std=gnu99 -c ccd_common.c -o ccd_common.o ccd_common.c: In function 'ccd_common': ccd_common.c:118:2: warning: #warning Using R fortran BLAS calls gcc -I"D:/RCompile/recent/R-2.13.0/include" -I"d:/Rcompile/CRANpkg/extralibs/local/include" -O3 -Wall -std=gnu99 -c ccd_r.c -o ccd_r.o ccd_r.c: In function 'ccd': ccd_r.c:163:5: warning: too many arguments for format ccd_r.c:156:7: warning: unused variable 'ret' ccd_r.c:18:11: warning: 'X' may be used uninitialized in this function ccd_r.c:18:14: warning: 'y' may be used uninitialized in this function gcc -shared -s -static-libgcc -o lassoshooting.dll tmp.def ccd_common.o ccd_r.o -Ld:/Rcompile/CRANpkg/extralibs/local/lib -LD:/RCompile/recent/R-2.13.0/bin/i386 -lRblas -lgfortran -LD:/RCompile/recent/R-2.13.0/bin/i386 -lR installing to d:/RCompile/CRANguest/R-release/lib/lassoshooting/libs/i386 *** arch - x64 x86_64-w64-mingw32-gcc -I"D:/RCompile/recent/R-2.13.0/include" -I"d:/Rcompile/CRANpkg/extralibs64new/local/include" -O2 -Wall -std=gnu99 -c ccd_common.c -o ccd_common.o ccd_common.c: In function 'ccd_common': ccd_common.c:118:2: warning: #warning Using R fortran BLAS calls x86_64-w64-mingw32-gcc -I"D:/RCompile/recent/R-2.13.0/include" -I"d:/Rcompile/CRANpkg/extralibs64new/local/include" -O2 -Wall -std=gnu99 -c ccd_r.c -o ccd_r.o ccd_r.c: In function 'ccd': ccd_r.c:163:5: warning: too many arguments for format ccd_r.c:156:7: warning: unused variable 'ret' ccd_r.c:18:11: warning: 'X' may be used uninitialized in this function ccd_r.c:18:14: warning: 'y' may be used uninitialized in this function x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o lassoshooting.dll tmp.def ccd_common.o ccd_r.o -Ld:/Rcompile/CRANpkg/extralibs64new/local/lib -LD:/RCompile/recent/R-2.13.0/bin/x64 -lRblas -lgfortran -LD:/RCompile/recent/R-2.13.0/bin/x64 -lR installing to d:/RCompile/CRANguest/R-release/lib/lassoshooting/libs/x64 ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'lassoshooting' as lassoshooting_0.1.3-6.zip * DONE (lassoshooting) __ 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] useDynLib in older versions e.g. (2.10)
Dear R-devel,
I investigated further by tracing into library.dynam.
The .dll file export a symbol "ccd". In e.g. R 2.8.1 the following
command succeeds,
dyn.load('/Program
Files/R/R-2.8.1/library/lassoshooting/libs/i386/lassoshooting.dll')
and the external symbol "ccd" becomes available.
However, inside library.dynam it doesn't add i386 to the path because
.Platform$r_arch is "". One way would be to re-zip the package with a
copy of the i386 version outside of the i386 directory, directly under
libs. That would work, but then I know I cannot commit a binary package
to CRAN. I guess I'm not the only one having this problem.
Happy easter, Tobias
--
Tobias Abenius
Ph.D. Student, M.Sc. in Computer Science
Mathematical Statistics
Mathematical Sciences
University of Gothenburg
On 04/20/2011 01:30 PM, Tobias Abenius wrote:
Hi,
Has something changed regarding the useDynLib in the NAMESPACE file in
packages? I've written a package that works in e.g. 2.12/2.13 but simply
cannot find the dynamic library under windows. The version on CRAN is
older than the one I'm talking about and depends on a newer version of R
but I want to make the package available to people with older versions.
> utils:::menuInstallLocal()
package 'lassoshooting' successfully unpacked and MD5 sums checked
> require(lassoshooting)
Loading required package: lassoshooting
Error in library.dynam(lib, package, package.lib) :
shared library 'lassoshooting' not found
In addition: Warning message:
package 'lassoshooting' was built under R version 2.13.0
I'm usually under linux and don't know about the gory details of .dll
files.
NAMESPACE file
--
useDynLib(lassoshooting)
export(lassoshooting)
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Re: [Rd] useDynLib in older versions e.g. (2.10)
On 21.04.2011 11:30, Tobias Abenius wrote:
Dear R-devel,
I investigated further by tracing into library.dynam.
The .dll file export a symbol "ccd". In e.g. R 2.8.1 the following
command succeeds,
dyn.load('/Program
Files/R/R-2.8.1/library/lassoshooting/libs/i386/lassoshooting.dll')
and the external symbol "ccd" becomes available.
However, inside library.dynam it doesn't add i386 to the path because
.Platform$r_arch is "". One way would be to re-zip the package with a
copy of the i386 version outside of the i386 directory, directly under
libs. That would work, but then I know I cannot commit a binary package
to CRAN. I guess I'm not the only one having this problem.
Happy easter, Tobias
I think you are mislead:
CRAN accepts source packages only. Binaries are made by CRAN (or more
particular by myself in Dortmund). For new packages or updates as of
today, we make binaries for R-2.12.x and R-2.13.x available. Note that
between major releases of R, you cannot assume that packages will work.
The help system changed in R-2.10.x (and no binaries are compatible
before vs. after the R-2.10.0 version) and the location of libraries in
R-2.12.x changed under Windows.
If you need a binary for R-2.8.x, you will have to INSTALL from sources
with R-2.8.x, otherwise we cannot guarantee compatibility. Note that
R-2.8.1 is unsupported and 5 major releases back!
Uwe Ligges
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[Rd] R CMD Sweave versus Sweave() on Windows
Dear list subscriber,
I am quite puzzled by the behaviour of processing Sweave files within an R
session, i.e.
Sweave("foo.Rnw") versus R CMD Sweave foo.Rnw
In the former the environmental variable 'SWEAVE_STYLEPATH_DEFAULT = TRUE' is
obeyed (this is set in etc/Renviron.site as well as under the users home
directory in .Renviron). That is the hard-coded path to Sweave.sty is included
in the resultant tex-file, whereas if the Sweave file is processed from cmd.exe
as R CMD Sweave foo.Rnw, only \usepackage{Sweave} is included.
Any pointers are much appreciated.
Best,
Bernhard
Output of sessionInfo():
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics datasets grDevices utils methods base
other attached packages:
[1] fortunes_1.4-1
Dr. Bernhard Pfaff
Director
Global Asset Allocation
Invesco Asset Management Deutschland GmbH
An der Welle 5
D-60322 Frankfurt am Main
Tel: +49 (0)69 29807 230
Fax: +49 (0)69 29807 178
www.institutional.invesco.com
Email: bernhard_pf...@fra.invesco.com
Geschäftsführer: Karl Georg Bayer, Bernhard Langer, Dr. Jens Langewand,
Alexander Lehmann, Christian Puschmann
Handelsregister: Frankfurt am Main, HRB 28469
Sitz der Gesellschaft: Frankfurt am Main
*
Confidentiality Note: The information contained in this ...{{dropped:10}}
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Re: [Rd] FW: [Rcpp-devel] Question on 5.6 Interfacing C++ code
On 11-04-20 11:33 AM, Sean Robert McGuffee wrote:
Hi, apparently I sent my question about using R and C++ to the wrong list,
ironically seeing as that list was called Rcpp. Anyway, I was directed to
post my question here. To summarize my current question, I have found two
commands that I want to be able to put into a package. The commands are 'R
CMD SHLIB X.cc X_main.cc' and
'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),' which I would like to
run when my package is installed and maybe have the second command run again
when my package is to be used. I've been trying to figure out the
documentation and learn through examples, but I'm just not getting it and
have been trying for weeks.
Does anyone on this site have any suggestions for me?
Assuming those lines work on their own, just do the following:
1. Put those *.cc files into the src directory of your package. (You
may need to create it.)
2. Put useDynLib(foo) into the NAMESPACE file of your foo package.
3. Call those functions using .C("X", args, PACKAGE="foo").
That's it.
Duncan Murdoch
Thanks, Sean
|On 20 April 2011 at 10:20, Sean Robert McGuffee wrote:
|
|
| Hi, thanks!
|
|>On 4/20/11 10:03 AM, "Steve Lianoglou"
wrote:
|> Hi,
|>
|> On Wed, Apr 20, 2011 at 9:49 AM, Sean Robert McGuffee
|>wrote:
|>> Hi, I have a quick couple of questions about some of the documentation
on
|>> the web page:
|>>
http://cran.r-project.org/doc/manuals/R-exts.html#Linking-GUIs-and-other-fro
n
|>> t_002dends-to-R
|>> under the heading:
|>> 5.6 Interfacing C++ code
|>>
|>> Question 1:
|>> If I¹m at a terminal, I can type the instructions they suggest:
|>> R CMD SHLIB X.cc X_main.cc
|>> If I wanted a package to do this, how would I tell the package to do
that
|>> same thing?
|>
|> Just to make sure we're all on the same page, you want an R package to
|> compile some source code into a shared library/dll from inside R?
|>
|> Not sure if there's a "baked in" way for that to happen, but maybe you
|> can invoke `R CMD WHATEVER` from inside R using the `system` function:
|>
|> R> ?system
|>
|
| ok, so where in the package would I put the system call in the package to
| have it run when installing the package?
You don't. As I said, 'R CMD INSTALL' et all do that.
Download an existing package with source, install it. Study its sources,
study the 'Writing R Extensions' manual. Ask on r-devel.
Basic R questions are off-topic here.
|>> Would I use the same command and just include it in a file somewhere in
the
|>> package?
|>> If so, which file?
|>
|> Hmm ... I'm curious what you're trying to do, exactly?
|
| I'm trying to figure out how take commands such as " R CMD SHLIB X.cc
| X_main.cc" followed by "dyn.load(paste("X", .Platform$dynlib.ext, sep =
| ""))," which are commands I can get to work for myself as a human
| interactively, and put the commands into a package to be automatically run
| when installing the package. I mean, it's great if I can compile a c++
file
| and then use it inside R, but I'm only doing that so I can let other
people
| do that via a package. As much as I read this documentation, I keep
missing
Again, I like working from an existing, working package. As I said, there are
almost 1000 to pick from.
Please direct follow-ups that have no bearing on Rcpp to r-devel.
Dirk
I've tried to figure this out for weeks by looking at other packages and
reading the confusing and nonintegrated documentation, but it hasn't taught
me how to put the two commands into a package so that they are run when the
package is installed. I'm simply trying to find out where in my package I
should put the commands 'R CMD SHLIB X.cc X_main.cc' and
'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),'
in order to have them run when my package is installed.
| the connections between the different sections. This is a section I am
| loving because it works very well. Thus, I want to figure out how to take
| the baby steps I'm doing and combine them into a package. Specifically, I
| want to take these two commands and insert them into a package so that
these
| commands will compile my code and make a dynamic ".so" file where R can
| access its functions when others install my package.
|
|>
|>> Question 2:
|>> dyn.load(paste("X", .Platform$dynlib.ext, sep = ""))
|>>
|>> Where does .Platform$dynlib.ext come from?
|>> What does it mean?
|>> What do it¹s components .Platform and $dynlib and .ext mean?
|>
|> .Platform is lust a normal list -- it is defined internally (I guess).
|> You can access "named" elements of a list with `$`.
|>
|> .Platform$dynlyb (or .Platform[['dynlib']]) tells you the extension
|> your particular system uses for shared libraries:
|>
|> R> .Platform
|> $OS.type
|> [1] "unix"
|>
|> $file.sep
|> [1] "/"
|>
|> $dynlib.ext
|> [1] ".so"
|>
|> $GUI
|> [1] "X11"
|>
|> $endian
|> [1] "little"
|>
|> $pkgType
|> [1] "mac.binary.leopard"
|>
|> $path.sep
|> [1] ":"
|>
|> $r_arch
|> [1] "x86_64"
|>
|> See
Re: [Rd] R CMD Sweave versus Sweave() on Windows
Bernd
.Renviron is not being read when you do R CMD ... This is documented,
but still puzzling to me. I solved this by using
Sys.setenv("SWEAVE_STYLEPATH_DEFAULT" = "TRUE")
in my .Rprofile (which is being read by R CMD ...). If you were on
linux you could also put it inside your shell profile (like ,.bashrc).
Kasper
On Thu, Apr 21, 2011 at 6:44 AM, Pfaff, Bernhard Dr.
wrote:
> Dear list subscriber,
>
> I am quite puzzled by the behaviour of processing Sweave files within an R
> session, i.e.
> Sweave("foo.Rnw") versus R CMD Sweave foo.Rnw
>
> In the former the environmental variable 'SWEAVE_STYLEPATH_DEFAULT = TRUE' is
> obeyed (this is set in etc/Renviron.site as well as under the users home
> directory in .Renviron). That is the hard-coded path to Sweave.sty is
> included in the resultant tex-file, whereas if the Sweave file is processed
> from cmd.exe as R CMD Sweave foo.Rnw, only \usepackage{Sweave} is included.
>
> Any pointers are much appreciated.
> Best,
> Bernhard
>
> Output of sessionInfo():
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
> [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
> [5] LC_TIME=German_Germany.1252
>
> attached base packages:
> [1] stats graphics datasets grDevices utils methods base
>
> other attached packages:
> [1] fortunes_1.4-1
>
>
> Dr. Bernhard Pfaff
> Director
> Global Asset Allocation
>
> Invesco Asset Management Deutschland GmbH
> An der Welle 5
> D-60322 Frankfurt am Main
>
> Tel: +49 (0)69 29807 230
> Fax: +49 (0)69 29807 178
> www.institutional.invesco.com
> Email: bernhard_pf...@fra.invesco.com
>
> Geschäftsführer: Karl Georg Bayer, Bernhard Langer, Dr. Jens Langewand,
> Alexander Lehmann, Christian Puschmann
> Handelsregister: Frankfurt am Main, HRB 28469
> Sitz der Gesellschaft: Frankfurt am Main
>
>
> *
> Confidentiality Note: The information contained in this ...{{dropped:10}}
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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Re: [Rd] How to get R to compile with PNG support
On 20 April 2011 at 12:16, Karl-Dieter Crisman wrote: | | | R is now configured for i686-pc-linux-gnu | Source directory: . | Installation directory:/home/sageserver/sage/local | C compiler:gcc -std=gnu99 | -I/home/sageserver/sage/local/include | -L/home/sageserver/sage/local/lib/ Fortran 77 compiler: | sage_fortran -g -O2 | C++ compiler: g++ -g -O2 | Fortran 90/95 compiler:sage_fortran -g -O2 Obj-C compiler: | Interfaces supported: X11 | External libraries:readline, BLAS(ATLAS), LAPACK(generic) | Additional capabilities: PNG, NLS | Options enabled: shared R library, R profiling | Recommended packages: yes | | | However: | | | > capabilities() |jpeg png tifftcltk X11 aqua http/ftp sockets | FALSEFALSEFALSEFALSEFALSEFALSE TRUE TRUE | | libxml fifo clediticonv NLS profmemcairo |TRUE TRUE TRUE TRUE TRUEFALSEFALSE Random guess: did you connect via ssh without x11 forwarding? I cannot see how configure find png.h and libpng but the binary fails. As all other X11 related formats are also shown false, methinks you are without a valid DISPLAY. That is actually an issue related to your headless use---which is what Sage may default too; see the R FAQ on this and the prior discussion on the xvfb-run wrapper which 'simulates' an x11 environment (which you need for png). So maybe you should revisit the Cairo devices---they allow you plotting without an x11 device (and also give you SVG). Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.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
On 21 April 2011 at 07:16, Duncan Murdoch wrote:
| On 11-04-20 11:33 AM, Sean Robert McGuffee wrote:
| > Hi, apparently I sent my question about using R and C++ to the wrong list,
| > ironically seeing as that list was called Rcpp. Anyway, I was directed to
| > post my question here. To summarize my current question, I have found two
| > commands that I want to be able to put into a package. The commands are 'R
| > CMD SHLIB X.cc X_main.cc' and
| > 'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),' which I would like to
| > run when my package is installed and maybe have the second command run again
| > when my package is to be used. I've been trying to figure out the
| > documentation and learn through examples, but I'm just not getting it and
| > have been trying for weeks.
| > Does anyone on this site have any suggestions for me?
|
| Assuming those lines work on their own, just do the following:
|
| 1. Put those *.cc files into the src directory of your package. (You
| may need to create it.)
|
| 2. Put useDynLib(foo) into the NAMESPACE file of your foo package.
|
| 3. Call those functions using .C("X", args, PACKAGE="foo").
|
| That's it.
We told Sean this twice or three times already over in this thread
http://thread.gmane.org/gmane.comp.lang.r.rcpp/1808
but the message does not seem to sink in. He keeps asking where to put 'R
CMD SHLIB' and doesn't seem to hear when we say there is none in a package...
Dirk
| Duncan Murdoch
|
| > Thanks, Sean
| >
| > |On 20 April 2011 at 10:20, Sean Robert McGuffee wrote:
| > |
| > |
| > | Hi, thanks!
| > |
| > |>On 4/20/11 10:03 AM, "Steve Lianoglou"
| > wrote:
| > |> Hi,
| > |>
| > |> On Wed, Apr 20, 2011 at 9:49 AM, Sean Robert McGuffee
| > |>wrote:
| > |>> Hi, I have a quick couple of questions about some of the documentation
| > on
| > |>> the web page:
| > |>>
| > http://cran.r-project.org/doc/manuals/R-exts.html#Linking-GUIs-and-other-fro
| > n
| > |>> t_002dends-to-R
| > |>> under the heading:
| > |>> 5.6 Interfacing C++ code
| > |>>
| > |>> Question 1:
| > |>> If I¹m at a terminal, I can type the instructions they suggest:
| > |>> R CMD SHLIB X.cc X_main.cc
| > |>> If I wanted a package to do this, how would I tell the package to do
| > that
| > |>> same thing?
| > |>
| > |> Just to make sure we're all on the same page, you want an R package to
| > |> compile some source code into a shared library/dll from inside R?
| > |>
| > |> Not sure if there's a "baked in" way for that to happen, but maybe you
| > |> can invoke `R CMD WHATEVER` from inside R using the `system` function:
| > |>
| > |> R> ?system
| > |>
| > |
| > | ok, so where in the package would I put the system call in the package to
| > | have it run when installing the package?
| >
| >> You don't. As I said, 'R CMD INSTALL' et all do that.
| >> Download an existing package with source, install it. Study its sources,
| >> study the 'Writing R Extensions' manual. Ask on r-devel.
| >> Basic R questions are off-topic here.
| >
| > |>> Would I use the same command and just include it in a file somewhere in
| > the
| > |>> package?
| > |>> If so, which file?
| > |>
| > |> Hmm ... I'm curious what you're trying to do, exactly?
| > |
| > | I'm trying to figure out how take commands such as " R CMD SHLIB X.cc
| > | X_main.cc" followed by "dyn.load(paste("X", .Platform$dynlib.ext, sep =
| > | ""))," which are commands I can get to work for myself as a human
| > | interactively, and put the commands into a package to be automatically run
| > | when installing the package. I mean, it's great if I can compile a c++
| > file
| > | and then use it inside R, but I'm only doing that so I can let other
| > people
| > | do that via a package. As much as I read this documentation, I keep
| > missing
| >
| >> Again, I like working from an existing, working package. As I said, there
are
| >> almost 1000 to pick from.
| >> Please direct follow-ups that have no bearing on Rcpp to r-devel.
| >> Dirk
| >
| > I've tried to figure this out for weeks by looking at other packages and
| > reading the confusing and nonintegrated documentation, but it hasn't taught
| > me how to put the two commands into a package so that they are run when the
| > package is installed. I'm simply trying to find out where in my package I
| > should put the commands 'R CMD SHLIB X.cc X_main.cc' and
| > 'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),'
| > in order to have them run when my package is installed.
| >
| >
| > | the connections between the different sections. This is a section I am
| > | loving because it works very well. Thus, I want to figure out how to take
| > | the baby steps I'm doing and combine them into a package. Specifically, I
| > | want to take these two commands and insert them into a package so that
| > these
| > | commands will compile my code and make a dynamic ".so" file where R can
| > | access its functions when others install my package.
| > |
| > |>
| > |>> Que
Re: [Rd] R CMD Sweave versus Sweave() on Windows
On Thu, 21 Apr 2011, Pfaff, Bernhard Dr. wrote:
Dear list subscriber,
I am quite puzzled by the behaviour of processing Sweave files within an R
session, i.e.
Sweave("foo.Rnw") versus R CMD Sweave foo.Rnw
In the former the environmental variable 'SWEAVE_STYLEPATH_DEFAULT =
TRUE' is obeyed (this is set in etc/Renviron.site as well as under
the users home directory in .Renviron). That is the hard-coded path
to Sweave.sty is included in the resultant tex-file, whereas if the
Sweave file is processed from cmd.exe as R CMD Sweave foo.Rnw, only
\usepackage{Sweave} is included.
Any pointers are much appreciated.
R CMD Sweave does not read the startup files. Try runnning
R --vanilla and Sweave("foo.Rnw"): you will see the same.
Best,
Bernhard
Output of sessionInfo():
sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics datasets grDevices utils methods base
other attached packages:
[1] fortunes_1.4-1
Dr. Bernhard Pfaff
Director
Global Asset Allocation
Invesco Asset Management Deutschland GmbH
An der Welle 5
D-60322 Frankfurt am Main
Tel: +49 (0)69 29807 230
Fax: +49 (0)69 29807 178
www.institutional.invesco.com
Email: bernhard_pf...@fra.invesco.com
Geschäftsführer: Karl Georg Bayer, Bernhard Langer, Dr. Jens Langewand,
Alexander Lehmann, Christian Puschmann
Handelsregister: Frankfurt am Main, HRB 28469
Sitz der Gesellschaft: Frankfurt am Main
*
Confidentiality Note: The information contained in this ...{{dropped:10}}
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Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595__
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Re: [Rd] BOOST libraries
(Redirected from r-packages, which is supposed to be an annoucements-only list, to r-devel which is for R development questions.) On 21 April 2011 at 08:10, Jay Emerson wrote: | We have used the BOOST interprocess libraries in package bigmemory | (and synchronicity, and ...) for about 3 years now. There is also a RQuantLib switched to using Boost when QuantLib did in June 2004, or almost seven years ago. | plan (more than tentative, but yet to actually happen) to provide a | package on CRAN that will provide these for more efficient use (having | multiple copies floating around across separate packages seems silly). | | If you are interested in this, please feel free to email me or Dirk | (and if you are not aware of Rcpp et. al. you should have a look | there, too). Cedric is a list member of rcpp-devel. | >I would like to know whether anyone had experience using the C++ Boost | >library within an R package, and how portable was the resulting package. Packages are perfectly portable as that is a main goal of Boost. So in that sense the question is misdirected; few things are as 'portable' as Boost. The issue is more about how to ensure _binary libraries_ are found if needed for linking. Boost itself is a (vast) collection of libraries (in the abstract sense of 'packages'), and only a few employ (binary) libraries. Many can be used in a pure template sense so that only headers are needed at compile time. That is what Jay refers to above: we are contemplating creating a common boost headers package to be used by the half dozen packages shipping their own copies. | >I am especially thinking of possible compiling problems on Windows and | >Apple systems. | | >If anyone had any tips on how to render an R package using Boost | >portable, that would be very much appreciated. Back to the issue of finding Boost libraries: you can study existing packages. RQuantLib for example needs to use a configure snippet and a special case on Windows. But in case you just want to use templates, look at RcppBDT --- an example package using Rcpp and its 'Rcpp modules' feature to easily access Boost Date_Time. It by choise does not use Date Time string parsing and formatting and hence uses only templated headers---and as such is easily buildable on Windows, OS X, ... as the CRAN page http://cran.r-project.org/package=RcppBDT and its links show. Hope this helps, Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD Sweave versus Sweave() on Windows
>
> On Thu, 21 Apr 2011, Pfaff, Bernhard Dr. wrote:
>
> > Dear list subscriber,
> >
> > I am quite puzzled by the behaviour of processing Sweave
> files within an R session, i.e.
> > Sweave("foo.Rnw") versus R CMD Sweave foo.Rnw
> >
> > In the former the environmental variable
> 'SWEAVE_STYLEPATH_DEFAULT =
> > TRUE' is obeyed (this is set in etc/Renviron.site as well
> as under the
> > users home directory in .Renviron). That is the hard-coded path to
> > Sweave.sty is included in the resultant tex-file, whereas if the
> > Sweave file is processed from cmd.exe as R CMD Sweave foo.Rnw, only
> > \usepackage{Sweave} is included.
> >
> > Any pointers are much appreciated.
>
> R CMD Sweave does not read the startup files. Try runnning R
> --vanilla and Sweave("foo.Rnw"): you will see the same.
Dear Prof. Ripley,
many thanks for your swift reply. This is indeed correct and educative --thanks
for this; but now I am kind of curious where this different behaviour compared
to version 2.12.0 has been announced or can be found? I have read the NEWS file
and the Windows specific NEWS of the latest release, but was not able to find
any pointer. That is, if I issue 'R CMD Sweave foo.Rnw' in cmd.exe with R
version 2.12.0, the hard-coded path to Sweave.sty is included and hence
environmental variables contained in the startup files are read.
Asked differently, is there a way such that R CMD Sweave does read the startup
files under R 2.13.0?
re: Kasper, many thanks for your reply. Incidentally, I have had
'Sys.setenv("SWEAVE_STYLEPATH_DEFAULT" = "TRUE")' directive already included in
my .Rprofile, but as Prof. Ripley correcly pointed out, these settings are not
taken effect.
Best,
Bernhard
>
> > Best,
> > Bernhard
> >
> > Output of sessionInfo():
> >> sessionInfo()
> > R version 2.13.0 (2011-04-13)
> > Platform: i386-pc-mingw32/i386 (32-bit)
> >
> > locale:
> > [1] LC_COLLATE=German_Germany.1252
> LC_CTYPE=German_Germany.1252 [3]
> > LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5]
> > LC_TIME=German_Germany.1252
> >
> > attached base packages:
> > [1] stats graphics datasets grDevices utils methods base
> >
> > other attached packages:
> > [1] fortunes_1.4-1
> >
> >
> > Dr. Bernhard Pfaff
> > Director
> > Global Asset Allocation
> >
> > Invesco Asset Management Deutschland GmbH An der Welle 5
> > D-60322 Frankfurt am Main
> >
> > Tel: +49 (0)69 29807 230
> > Fax: +49 (0)69 29807 178
> > www.institutional.invesco.com
> > Email: bernhard_pf...@fra.invesco.com
> >
> > Geschäftsführer: Karl Georg Bayer, Bernhard Langer, Dr. Jens
> > Langewand, Alexander Lehmann, Christian Puschmann
> > Handelsregister: Frankfurt am Main, HRB 28469 Sitz der
> Gesellschaft:
> > Frankfurt am Main
> >
> >
> > *
> > Confidentiality Note: The information contained in this
> > ...{{dropped:10}}
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> --
> Brian D. Ripley, rip...@stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UKFax: +44 1865 272595
>
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Re: [Rd] How to get R to compile with PNG support
On 04/19/2011 05:00 AM, r-devel-requ...@r-project.org wrote:
Date: Mon, 18 Apr 2011 11:48:40 -0400
From: Karl-Dieter Crisman
To:r-devel@r-project.org
Cc: Jason Grout
Subject: [Rd] How to get R to compile with PNG support
Message-ID:
Content-Type: text/plain; charset=windows-1252
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).
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).
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?
I had a similar question some time ago. The answer (of course) is in the
code and configure macros. The main logic is in
src/main/platform.c::do_capabilities:
SET_STRING_ELT(ansnames, i, mkChar("png"));
#ifdef HAVE_PNG
# if defined Unix && !defined HAVE_WORKING_CAIRO
LOGICAL(ans)[i++] = X11;
# else /* Windows */
LOGICAL(ans)[i++] = TRUE;
# endif
#else
LOGICAL(ans)[i++] = FALSE;
#endif
---
From m4/R.m4:
if test "${use_libpng}" = yes; then
AC_CHECK_LIB(z, main, [have_png=yes], [have_png=no])
if test "${have_png}" = yes; then
_R_HEADER_PNG
have_png=${r_cv_header_png_h}
fi
if test "${have_png}" = yes; then
AC_CHECK_LIB(png, png_create_write_struct,
[have_png=yes],
[have_png=no],
[-lz ${LIBS}])
fi
if test "${have_png}" = yes; then
BITMAP_LIBS="${BITMAP_LIBS} -lpng -lz"
AC_DEFINE(HAVE_PNG, 1,
[Define if you have the PNG headers and libraries.])
fi
fi
---
HAVE_WORKING_CAIRO is set by m4/cairo.m4. However, the PNG function
doesn't consult capabilities("png"). Presumably capabilities("png") is
sufficient, but you'll have to pick up the trail in the png function to
find out what's really going on.
I've had good outcomes with cairo.
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
--
Matthew S Shotwell Assistant Professor School of Medicine
Departme
Re: [Rd] R CMD Sweave versus Sweave() on Windows
On Thu, Apr 21, 2011 at 6:44 AM, Pfaff, Bernhard Dr.
wrote:
> Dear list subscriber,
>
> I am quite puzzled by the behaviour of processing Sweave files within an R
> session, i.e.
> Sweave("foo.Rnw") versus R CMD Sweave foo.Rnw
>
> In the former the environmental variable 'SWEAVE_STYLEPATH_DEFAULT = TRUE' is
> obeyed (this is set in etc/Renviron.site as well as under the users home
> directory in .Renviron). That is the hard-coded path to Sweave.sty is
> included in the resultant tex-file, whereas if the Sweave file is processed
> from cmd.exe as R CMD Sweave foo.Rnw, only \usepackage{Sweave} is included.
>
> Any pointers are much appreciated.
> Best,
> Bernhard
>
> Output of sessionInfo():
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
> [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
> [5] LC_TIME=German_Germany.1252
>
> attached base packages:
> [1] stats graphics datasets grDevices utils methods base
>
> other attached packages:
> [1] fortunes_1.4-1
>
SWEAVE_STYLEPATH_DEFAULT is automatically set in Sweave.bat found here
(its part of the batchfiles distribution but does not require any
other batch file in order to run it):
http://batchfiles.googlecode.com/svn/trunk/Sweave.bat
This was only just added and has not been tested yet but if anyone
would like to try it just put it anywhere on your Windows PATH (or
current directory) and issue a command like this from the Windows
console:
Sweave myfile.Rnw
--
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
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Re: [Rd] How to get R to compile with PNG support
Thanks for your replies, Dirk and Matt. On Thu, Apr 21, 2011 at 7:49 AM, Dirk Eddelbuettel wrote: > > On 20 April 2011 at 12:16, Karl-Dieter Crisman wrote: > | > | > | R is now configured for i686-pc-linux-gnu > | Source directory: . > | Installation directory: /home/sageserver/sage/local > | C compiler: gcc -std=gnu99 > | -I/home/sageserver/sage/local/include > | -L/home/sageserver/sage/local/lib/ Fortran 77 compiler: > | sage_fortran -g -O2 > | C++ compiler: g++ -g -O2 > | Fortran 90/95 compiler: sage_fortran -g -O2 Obj-C compiler: > | Interfaces supported: X11 > | External libraries: readline, BLAS(ATLAS), LAPACK(generic) > | Additional capabilities: PNG, NLS > | Options enabled: shared R library, R profiling > | Recommended packages: yes > | > | > | However: > | > | > | > capabilities() > | jpeg png tiff tcltk X11 aqua http/ftp sockets > | FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE > | > | libxml fifo cledit iconv NLS profmem cairo > | TRUE TRUE TRUE TRUE TRUE FALSE FALSE > > Random guess: did you connect via ssh without x11 forwarding? Almost certainly, yes. (I am an interlocutor right now for someone who is actually doing this, my apologies.) But it's a machine we just ssh into, I'm pretty sure, though it does serve up web pages. > I cannot see how configure find png.h and libpng but the binary fails. As all > other X11 related formats are also shown false, methinks you are without a > valid DISPLAY. That is quite likely. So it sounds like for png() to be set to use the X11 device, there has to (somewhere) be a visual output - presumably that is the part LOGICAL(ans)[i++] = X11; in Matt's answer. > That is actually an issue related to your headless use---which is what Sage > may default too; see the R FAQ on this and the prior discussion on the > xvfb-run wrapper which 'simulates' an x11 environment (which you need for > png). So maybe you should revisit the Cairo devices---they allow you > plotting without an x11 device (and also give you SVG). > Yeah, and I saw your SO answer on this (after the fact) as well. In some sense, we are just trying to get graphics on one machine. Note that we have installed the cairo devel package on this very machine, but it's not being picked up - maybe it's looking in the wrong place? That is one of the reasons this is confusing. But in a larger sense, because of Sage's "batteries included" philosophy (which we know not everyone agrees with!), we would like to have a one-shot way so that *everyone* will see R graphics, not just people whose binary happens to have been compiled on a machine that has X and a display. If that means adding 22.5 MB to our tarball for Cairo... maybe, maybe not. I won't copy Matt's message here, but I appreciate the pointers to exactly where these things are defined very much - without knowing where to look, it would be a long slog. Hopefully we'll have some success! Thanks for the replies, and for any other ideas. Karl-Dieter __ 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
On 21 April 2011 at 09:51, Karl-Dieter Crisman wrote: | Thanks for your replies, Dirk and Matt. My pleasure. | On Thu, Apr 21, 2011 at 7:49 AM, Dirk Eddelbuettel wrote: | > Random guess: did you connect via ssh without x11 forwarding? | | Almost certainly, yes. (I am an interlocutor right now for someone | who is actually doing this, my apologies.) | But it's a machine we just ssh into, I'm pretty sure, though it does | serve up web pages. [...] | In some sense, we are just trying to get graphics on one machine. | Note that we have installed the cairo devel package on this very | machine, but it's not being picked up - maybe it's looking in the | wrong place? That is one of the reasons this is confusing. You have to understand that even though this problem may seem urgent and novel to you and the Sage team, it is actually about as old as the web and R itself. In a nutshell, we all (in the people reading r-help and r-devel sense) have been explaining to folks since the late 1990s that in order to run png() to 'just create some charts for a webserver' ... you need an X11 server because that is where the font metrics come from. Or else no png for you. | But in a larger sense, because of Sage's "batteries included" | philosophy (which we know not everyone agrees with!), we would like to | have a one-shot way so that *everyone* will see R graphics, not just | people whose binary happens to have been compiled on a machine that | has X and a display. If that means adding 22.5 MB to our tarball for | Cairo... maybe, maybe not. As they say: "There is no such thing as a free lunch." Pick an X11 server (to be able to launch the 'xvfb-run' wrapper) for font metrics, or run something else like Cairo. Neither one is real cheap. Such is life. System such as Sage become so large because having things like this around on all deployment systems implies (at least to some degree) replicating fundamental OS level features because they unfortunately have supply things missing or broken across OSs. Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.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
On Apr 21, 2011, at 9:51 AM, Karl-Dieter Crisman wrote: > Thanks for your replies, Dirk and Matt. > > On Thu, Apr 21, 2011 at 7:49 AM, Dirk Eddelbuettel wrote: >> >> On 20 April 2011 at 12:16, Karl-Dieter Crisman wrote: >> | >> | >> | R is now configured for i686-pc-linux-gnu >> | Source directory: . >> | Installation directory:/home/sageserver/sage/local >> | C compiler:gcc -std=gnu99 >> | -I/home/sageserver/sage/local/include >> | -L/home/sageserver/sage/local/lib/ Fortran 77 compiler: >> | sage_fortran -g -O2 >> | C++ compiler: g++ -g -O2 >> | Fortran 90/95 compiler:sage_fortran -g -O2 Obj-C compiler: >> | Interfaces supported: X11 >> | External libraries:readline, BLAS(ATLAS), LAPACK(generic) >> | Additional capabilities: PNG, NLS >> | Options enabled: shared R library, R profiling >> | Recommended packages: yes >> | >> | >> | However: >> | >> | >> | > capabilities() >> |jpeg png tifftcltk X11 aqua http/ftp sockets >> | FALSEFALSEFALSEFALSEFALSEFALSE TRUE TRUE >> | >> | libxml fifo clediticonv NLS profmemcairo >> |TRUE TRUE TRUE TRUE TRUEFALSEFALSE >> >> Random guess: did you connect via ssh without x11 forwarding? > > Almost certainly, yes. (I am an interlocutor right now for someone > who is actually doing this, my apologies.) > But it's a machine we just ssh into, I'm pretty sure, though it does > serve up web pages. > >> I cannot see how configure find png.h and libpng but the binary fails. As all >> other X11 related formats are also shown false, methinks you are without a >> valid DISPLAY. > > That is quite likely. So it sounds like for png() to be set to use > the X11 device, there has to (somewhere) be a visual output - > presumably that is the part LOGICAL(ans)[i++] = X11; in Matt's answer. > >> That is actually an issue related to your headless use---which is what Sage >> may default too; see the R FAQ on this and the prior discussion on the >> xvfb-run wrapper which 'simulates' an x11 environment (which you need for >> png). So maybe you should revisit the Cairo devices---they allow you >> plotting without an x11 device (and also give you SVG). >> > > Yeah, and I saw your SO answer on this (after the fact) as well. > > In some sense, we are just trying to get graphics on one machine. > Note that we have installed the cairo devel package on this very > machine, but it's not being picked up - maybe it's looking in the > wrong place? That is one of the reasons this is confusing. > > But in a larger sense, because of Sage's "batteries included" > philosophy (which we know not everyone agrees with!), we would like to > have a one-shot way so that *everyone* will see R graphics, not just > people whose binary happens to have been compiled on a machine that > has X and a display. If that means adding 22.5 MB to our tarball for > Cairo... maybe, maybe not. > Maybe yes in that case - that's what we do in Mac binaries -- and on Mac users always expect "batteries included" so we include libcairo statically. (The same applies for R packages like Cairo which provides png support independent of X11). Cheers, Simon > I won't copy Matt's message here, but I appreciate the pointers to > exactly where these things are defined very much - without knowing > where to look, it would be a long slog. Hopefully we'll have some > success! Thanks for the replies, and for any other ideas. > > Karl-Dieter > > __ > 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] FW: [Rcpp-devel] Question on 5.6 Interfacing C++ code
Thanks,
That's great, but I don't know how to determine what foo is. How do I
declare the name of the package?
On 4/21/11 7:16 AM, "Duncan Murdoch" wrote:
> On 11-04-20 11:33 AM, Sean Robert McGuffee wrote:
>> Hi, apparently I sent my question about using R and C++ to the wrong list,
>> ironically seeing as that list was called Rcpp. Anyway, I was directed to
>> post my question here. To summarize my current question, I have found two
>> commands that I want to be able to put into a package. The commands are 'R
>> CMD SHLIB X.cc X_main.cc' and
>> 'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),' which I would like to
>> run when my package is installed and maybe have the second command run again
>> when my package is to be used. I've been trying to figure out the
>> documentation and learn through examples, but I'm just not getting it and
>> have been trying for weeks.
>> Does anyone on this site have any suggestions for me?
>
> Assuming those lines work on their own, just do the following:
>
> 1. Put those *.cc files into the src directory of your package. (You
> may need to create it.)
>
> 2. Put useDynLib(foo) into the NAMESPACE file of your foo package.
>
> 3. Call those functions using .C("X", args, PACKAGE="foo").
>
> That's it.
>
> Duncan Murdoch
>
>> Thanks, Sean
>>
>> |On 20 April 2011 at 10:20, Sean Robert McGuffee wrote:
>> |
>> |
>> | Hi, thanks!
>> |
>> |>On 4/20/11 10:03 AM, "Steve Lianoglou"
>> wrote:
>> |> Hi,
>> |>
>> |> On Wed, Apr 20, 2011 at 9:49 AM, Sean Robert McGuffee
>> |>wrote:
>> |>> Hi, I have a quick couple of questions about some of the documentation
>> on
>> |>> the web page:
>> |>>
>> http://cran.r-project.org/doc/manuals/R-exts.html#Linking-GUIs-and-other-fro
>> n
>> |>> t_002dends-to-R
>> |>> under the heading:
>> |>> 5.6 Interfacing C++ code
>> |>>
>> |>> Question 1:
>> |>> If I¹m at a terminal, I can type the instructions they suggest:
>> |>> R CMD SHLIB X.cc X_main.cc
>> |>> If I wanted a package to do this, how would I tell the package to do
>> that
>> |>> same thing?
>> |>
>> |> Just to make sure we're all on the same page, you want an R package to
>> |> compile some source code into a shared library/dll from inside R?
>> |>
>> |> Not sure if there's a "baked in" way for that to happen, but maybe you
>> |> can invoke `R CMD WHATEVER` from inside R using the `system` function:
>> |>
>> |> R> ?system
>> |>
>> |
>> | ok, so where in the package would I put the system call in the package to
>> | have it run when installing the package?
>>
>>> You don't. As I said, 'R CMD INSTALL' et all do that.
>>> Download an existing package with source, install it. Study its sources,
>>> study the 'Writing R Extensions' manual. Ask on r-devel.
>>> Basic R questions are off-topic here.
>>
>> |>> Would I use the same command and just include it in a file somewhere in
>> the
>> |>> package?
>> |>> If so, which file?
>> |>
>> |> Hmm ... I'm curious what you're trying to do, exactly?
>> |
>> | I'm trying to figure out how take commands such as " R CMD SHLIB X.cc
>> | X_main.cc" followed by "dyn.load(paste("X", .Platform$dynlib.ext, sep =
>> | ""))," which are commands I can get to work for myself as a human
>> | interactively, and put the commands into a package to be automatically run
>> | when installing the package. I mean, it's great if I can compile a c++
>> file
>> | and then use it inside R, but I'm only doing that so I can let other
>> people
>> | do that via a package. As much as I read this documentation, I keep
>> missing
>>
>>> Again, I like working from an existing, working package. As I said, there
>>> are
>>> almost 1000 to pick from.
>>> Please direct follow-ups that have no bearing on Rcpp to r-devel.
>>> Dirk
>>
>> I've tried to figure this out for weeks by looking at other packages and
>> reading the confusing and nonintegrated documentation, but it hasn't taught
>> me how to put the two commands into a package so that they are run when the
>> package is installed. I'm simply trying to find out where in my package I
>> should put the commands 'R CMD SHLIB X.cc X_main.cc' and
>> 'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),'
>> in order to have them run when my package is installed.
>>
>>
>> | the connections between the different sections. This is a section I am
>> | loving because it works very well. Thus, I want to figure out how to take
>> | the baby steps I'm doing and combine them into a package. Specifically, I
>> | want to take these two commands and insert them into a package so that
>> these
>> | commands will compile my code and make a dynamic ".so" file where R can
>> | access its functions when others install my package.
>> |
>> |>
>> |>> Question 2:
>> |>> dyn.load(paste("X", .Platform$dynlib.ext, sep = ""))
>> |>>
>> |>> Where does .Platform$dynlib.ext come from?
>> |>> What does it mean?
>> |>> What do it¹s components .Platform and $dynlib and .ext mean?
>> |>
>> |> .Platform is lust a normal li
Re: [Rd] FW: [Rcpp-devel] Question on 5.6 Interfacing C++ code
On Apr 21, 2011, at 10:52 AM, Sean Robert McGuffee wrote:
> Thanks,
> That's great, but I don't know how to determine what foo is.
It's the name of your package.
> How do I declare the name of the package?
>
in DESCRIPTION:
Package: name
and the directory of your package has to have the same name - please do read
http://r.research.att.com/man/R-exts.html#Creating-R-packages
Cheers,
Simon
>
> On 4/21/11 7:16 AM, "Duncan Murdoch" wrote:
>
>> On 11-04-20 11:33 AM, Sean Robert McGuffee wrote:
>>> Hi, apparently I sent my question about using R and C++ to the wrong list,
>>> ironically seeing as that list was called Rcpp. Anyway, I was directed to
>>> post my question here. To summarize my current question, I have found two
>>> commands that I want to be able to put into a package. The commands are 'R
>>> CMD SHLIB X.cc X_main.cc' and
>>> 'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),' which I would like to
>>> run when my package is installed and maybe have the second command run again
>>> when my package is to be used. I've been trying to figure out the
>>> documentation and learn through examples, but I'm just not getting it and
>>> have been trying for weeks.
>>> Does anyone on this site have any suggestions for me?
>>
>> Assuming those lines work on their own, just do the following:
>>
>> 1. Put those *.cc files into the src directory of your package. (You
>> may need to create it.)
>>
>> 2. Put useDynLib(foo) into the NAMESPACE file of your foo package.
>>
>> 3. Call those functions using .C("X", args, PACKAGE="foo").
>>
>> That's it.
>>
>> Duncan Murdoch
>>
>>> Thanks, Sean
>>>
>>> |On 20 April 2011 at 10:20, Sean Robert McGuffee wrote:
>>> |
>>> |
>>> | Hi, thanks!
>>> |
>>> |>On 4/20/11 10:03 AM, "Steve Lianoglou"
>>> wrote:
>>> |> Hi,
>>> |>
>>> |> On Wed, Apr 20, 2011 at 9:49 AM, Sean Robert McGuffee
>>> |>wrote:
>>> |>> Hi, I have a quick couple of questions about some of the documentation
>>> on
>>> |>> the web page:
>>> |>>
>>> http://cran.r-project.org/doc/manuals/R-exts.html#Linking-GUIs-and-other-fro
>>> n
>>> |>> t_002dends-to-R
>>> |>> under the heading:
>>> |>> 5.6 Interfacing C++ code
>>> |>>
>>> |>> Question 1:
>>> |>> If I’m at a terminal, I can type the instructions they suggest:
>>> |>> R CMD SHLIB X.cc X_main.cc
>>> |>> If I wanted a package to do this, how would I tell the package to do
>>> that
>>> |>> same thing?
>>> |>
>>> |> Just to make sure we're all on the same page, you want an R package to
>>> |> compile some source code into a shared library/dll from inside R?
>>> |>
>>> |> Not sure if there's a "baked in" way for that to happen, but maybe you
>>> |> can invoke `R CMD WHATEVER` from inside R using the `system` function:
>>> |>
>>> |> R> ?system
>>> |>
>>> |
>>> | ok, so where in the package would I put the system call in the package to
>>> | have it run when installing the package?
>>>
You don't. As I said, 'R CMD INSTALL' et all do that.
Download an existing package with source, install it. Study its sources,
study the 'Writing R Extensions' manual. Ask on r-devel.
Basic R questions are off-topic here.
>>>
>>> |>> Would I use the same command and just include it in a file somewhere in
>>> the
>>> |>> package?
>>> |>> If so, which file?
>>> |>
>>> |> Hmm ... I'm curious what you're trying to do, exactly?
>>> |
>>> | I'm trying to figure out how take commands such as " R CMD SHLIB X.cc
>>> | X_main.cc" followed by "dyn.load(paste("X", .Platform$dynlib.ext, sep =
>>> | ""))," which are commands I can get to work for myself as a human
>>> | interactively, and put the commands into a package to be automatically run
>>> | when installing the package. I mean, it's great if I can compile a c++
>>> file
>>> | and then use it inside R, but I'm only doing that so I can let other
>>> people
>>> | do that via a package. As much as I read this documentation, I keep
>>> missing
>>>
Again, I like working from an existing, working package. As I said, there
are
almost 1000 to pick from.
Please direct follow-ups that have no bearing on Rcpp to r-devel.
Dirk
>>>
>>> I've tried to figure this out for weeks by looking at other packages and
>>> reading the confusing and nonintegrated documentation, but it hasn't taught
>>> me how to put the two commands into a package so that they are run when the
>>> package is installed. I'm simply trying to find out where in my package I
>>> should put the commands 'R CMD SHLIB X.cc X_main.cc' and
>>> 'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),'
>>> in order to have them run when my package is installed.
>>>
>>>
>>> | the connections between the different sections. This is a section I am
>>> | loving because it works very well. Thus, I want to figure out how to take
>>> | the baby steps I'm doing and combine them into a package. Specifically, I
>>> | want to take these two commands and insert them into a package so that
>>> these
>>> | commands w
Re: [Rd] FW: [Rcpp-devel] Question on 5.6 Interfacing C++ code
On 21/04/2011 10:52 AM, Sean Robert McGuffee wrote:
Thanks,
That's great, but I don't know how to determine what foo is. How do I
declare the name of the package?
See the Writing R Extensions manual, or a tutorial on the topic, e.g.
the one I gave at UseR 2008, available here:
www.r-project.org/conferences/*useR-2008*/slides/*Murdoch*.pdf
*
*It contains a few things that are no longer true (e.g. you don't need
Perl any more), but is mostly still accurate.
Duncan Murdoch
On 4/21/11 7:16 AM, "Duncan Murdoch" wrote:
> On 11-04-20 11:33 AM, Sean Robert McGuffee wrote:
>> Hi, apparently I sent my question about using R and C++ to the wrong list,
>> ironically seeing as that list was called Rcpp. Anyway, I was directed to
>> post my question here. To summarize my current question, I have found two
>> commands that I want to be able to put into a package. The commands are 'R
>> CMD SHLIB X.cc X_main.cc' and
>> 'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),' which I would like to
>> run when my package is installed and maybe have the second command run again
>> when my package is to be used. I've been trying to figure out the
>> documentation and learn through examples, but I'm just not getting it and
>> have been trying for weeks.
>> Does anyone on this site have any suggestions for me?
>
> Assuming those lines work on their own, just do the following:
>
> 1. Put those *.cc files into the src directory of your package. (You
> may need to create it.)
>
> 2. Put useDynLib(foo) into the NAMESPACE file of your foo package.
>
> 3. Call those functions using .C("X", args, PACKAGE="foo").
>
> That's it.
>
> Duncan Murdoch
>
>> Thanks, Sean
>>
>> |On 20 April 2011 at 10:20, Sean Robert McGuffee wrote:
>> |
>> |
>> | Hi, thanks!
>> |
>> |>On 4/20/11 10:03 AM, "Steve Lianoglou"
>> wrote:
>> |> Hi,
>> |>
>> |> On Wed, Apr 20, 2011 at 9:49 AM, Sean Robert McGuffee
>> |> wrote:
>> |>> Hi, I have a quick couple of questions about some of the documentation
>> on
>> |>> the web page:
>> |>>
>> http://cran.r-project.org/doc/manuals/R-exts.html#Linking-GUIs-and-other-fro
>> n
>> |>> t_002dends-to-R
>> |>> under the heading:
>> |>> 5.6 Interfacing C++ code
>> |>>
>> |>> Question 1:
>> |>> If I¹m at a terminal, I can type the instructions they suggest:
>> |>> R CMD SHLIB X.cc X_main.cc
>> |>> If I wanted a package to do this, how would I tell the package to do
>> that
>> |>> same thing?
>> |>
>> |> Just to make sure we're all on the same page, you want an R package to
>> |> compile some source code into a shared library/dll from inside R?
>> |>
>> |> Not sure if there's a "baked in" way for that to happen, but maybe you
>> |> can invoke `R CMD WHATEVER` from inside R using the `system` function:
>> |>
>> |> R> ?system
>> |>
>> |
>> | ok, so where in the package would I put the system call in the package to
>> | have it run when installing the package?
>>
>>> You don't. As I said, 'R CMD INSTALL' et all do that.
>>> Download an existing package with source, install it. Study its sources,
>>> study the 'Writing R Extensions' manual. Ask on r-devel.
>>> Basic R questions are off-topic here.
>>
>> |>> Would I use the same command and just include it in a file somewhere
in
>> the
>> |>> package?
>> |>> If so, which file?
>> |>
>> |> Hmm ... I'm curious what you're trying to do, exactly?
>> |
>> | I'm trying to figure out how take commands such as " R CMD SHLIB X.cc
>> | X_main.cc" followed by "dyn.load(paste("X", .Platform$dynlib.ext, sep =
>> | ""))," which are commands I can get to work for myself as a human
>> | interactively, and put the commands into a package to be automatically run
>> | when installing the package. I mean, it's great if I can compile a c++
>> file
>> | and then use it inside R, but I'm only doing that so I can let other
>> people
>> | do that via a package. As much as I read this documentation, I keep
>> missing
>>
>>> Again, I like working from an existing, working package. As I said, there
>>> are
>>> almost 1000 to pick from.
>>> Please direct follow-ups that have no bearing on Rcpp to r-devel.
>>> Dirk
>>
>> I've tried to figure this out for weeks by looking at other packages and
>> reading the confusing and nonintegrated documentation, but it hasn't taught
>> me how to put the two commands into a package so that they are run when the
>> package is installed. I'm simply trying to find out where in my package I
>> should put the commands 'R CMD SHLIB X.cc X_main.cc' and
>> 'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),'
>> in order to have them run when my package is installed.
>>
>>
>> | the connections between the different sections. This is a section I am
>> | loving because it works very well. Thus, I want to figure out how to take
>> | the baby steps I'm doing and combine them into a package. Specifically, I
>> | want to take these two
Re: [Rd] How to get R to compile with PNG support
On Apr 20, 2011, at 8:35 AM, Karl-Dieter Crisman wrote: >> Message: 12 >> Date: Wed, 20 Apr 2011 02:09:23 -0700 (PDT) >> From: Sharpie >> To: r-devel@r-project.org >> Subject: Re: [Rd] How to get R to compile with PNG support >> Message-ID: <1303290563237-3462502.p...@n4.nabble.com> >> Content-Type: text/plain; charset=UTF-8 >> >> >> 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. > > Good morning, Charlie et al., > > Thanks for your words. We like R, too! We need to advertise it more, > and this thread is part of making sure that happens in the long run. > > To the issue at hand. Our main concern is just not to have to spend > hours reading the configuration and makefile to figure out exactly > where things happen. > > >>> >>> 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. > > > True. It's the device enabling that I'm talking about. We enable > aqua on Mac, and png on Linux. > > We ignore Cairo, and ignore X11 on Mac because it is too touchy (at > least, according to the FAQ on this - different weird instructions for > each type, and of course not everyone has X on Mac). > FWIW this seem a little outdated - all recent OS X come with X11 installed and libcairo is not a problem to build ... >> 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. >> > > Great. That is okay with us; we aren't expecting (yet) people to be > able to save R graphics in various output formats. Our native > (matplotlib) graphics, we do expect this. > > >>> 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. >>> > > >> 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. > > Gotcha. I suspect that the X11 not listed under Interfaces is the > problem (again, we ignore Cairo). > > What is the *exact* file or directory that the R configure looks for > in trying to list X11 under Interfaces? And is there any way around > this at all? That is, is there any way for R to create but not > display a graphic if it has (for instance) png support, like the one > on the Trac ticket did? We can always just search for the png file > and serve it up in our own viewers. > > Note that we already search for /usr/include/X11/Xwindows.h, and > adding xorg-dev didn't help with the latest one (which may not be on > the Trac ticket). > I missed which distro you're using, but xorg-dev is likely insufficient (by design). For example on Debian you'll also need libxt-dev. Note that your best friend is config.log and the output of configure - that tells *exactly* what you're missing. You will need at least X11, ICE, Xt libraries and X11/Intrinsic.h headers. Cheers, Simon >> In the ask.sagemath question the problem appears to be that the user had
Re: [Rd] FW: [Rcpp-devel] Question on 5.6 Interfacing C++ code
So, how is the package turning it's name into those commands?
Does the installation automatically list the src directory and iteratively
run a loop over each file and call 'R CMD SHLIB objectOfIterator' ?
The reason this is so important is because it¹s easy to get things to work
via a terminal command 'R CMD SHLIB someSourceFile.cpp¹, so I want to be
able to take things that work that way and put them inside a package. It
seems peculiar to me that R needs to access functions through a C wrapper
too. I¹m not sure why it can¹t access C++ functions directly. What R is
doing is over my head because it is calling functions that were not compiled
into it. I mean, if I want to call a C or C++ function from C++ code, I have
to convince my compiler that I have a header and all definitions behind the
declarations in my source files to compile my own programs. I don¹t know how
R works when the program is compiled way in advance and is then somehow
calling on declarations made later in another place. I think objective C/C++
allows for this type of thing where you can write code to call something
that is declared but not yet defined. However, I¹m not sure what R is doing?
Is R doing the same thing a compiler would do and creating it¹s own binary
instructions for the launch of a function, or is it creating a new
executable and launching that as it¹s own application and then somehow
communicating with it?
Sean
On 4/21/11 7:52 AM, "Dirk Eddelbuettel" wrote:
>
> On 21 April 2011 at 07:16, Duncan Murdoch wrote:
> | On 11-04-20 11:33 AM, Sean Robert McGuffee wrote:
> | > Hi, apparently I sent my question about using R and C++ to the wrong list,
> | > ironically seeing as that list was called Rcpp. Anyway, I was directed to
> | > post my question here. To summarize my current question, I have found two
> | > commands that I want to be able to put into a package. The commands are 'R
> | > CMD SHLIB X.cc X_main.cc' and
> | > 'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),' which I would like to
> | > run when my package is installed and maybe have the second command run
> again
> | > when my package is to be used. I've been trying to figure out the
> | > documentation and learn through examples, but I'm just not getting it and
> | > have been trying for weeks.
> | > Does anyone on this site have any suggestions for me?
> |
> | Assuming those lines work on their own, just do the following:
> |
> | 1. Put those *.cc files into the src directory of your package. (You
> | may need to create it.)
> |
> | 2. Put useDynLib(foo) into the NAMESPACE file of your foo package.
> |
> | 3. Call those functions using .C("X", args, PACKAGE="foo").
> |
> | That's it.
>
> We told Sean this twice or three times already over in this thread
>
> http://thread.gmane.org/gmane.comp.lang.r.rcpp/1808
>
> but the message does not seem to sink in. He keeps asking where to put 'R
> CMD SHLIB' and doesn't seem to hear when we say there is none in a package...
>
> Dirk
>
> | Duncan Murdoch
> |
> | > Thanks, Sean
> | >
> | > |On 20 April 2011 at 10:20, Sean Robert McGuffee wrote:
> | > |
> | > |
> | > | Hi, thanks!
> | > |
> | > |>On 4/20/11 10:03 AM, "Steve Lianoglou"
> | > wrote:
> | > |> Hi,
> | > |>
> | > |> On Wed, Apr 20, 2011 at 9:49 AM, Sean Robert McGuffee
> | > |>wrote:
> | > |>> Hi, I have a quick couple of questions about some of the
> documentation
> | > on
> | > |>> the web page:
> | > |>>
> | >
> http://cran.r-project.org/doc/manuals/R-exts.html#Linking-GUIs-and-other-fro
> | > n
> | > |>> t_002dends-to-R
> | > |>> under the heading:
> | > |>> 5.6 Interfacing C++ code
> | > |>>
> | > |>> Question 1:
> | > |>> If I¹m at a terminal, I can type the instructions they suggest:
> | > |>> R CMD SHLIB X.cc X_main.cc
> | > |>> If I wanted a package to do this, how would I tell the package to do
> | > that
> | > |>> same thing?
> | > |>
> | > |> Just to make sure we're all on the same page, you want an R package to
> | > |> compile some source code into a shared library/dll from inside R?
> | > |>
> | > |> Not sure if there's a "baked in" way for that to happen, but maybe you
> | > |> can invoke `R CMD WHATEVER` from inside R using the `system` function:
> | > |>
> | > |> R> ?system
> | > |>
> | > |
> | > | ok, so where in the package would I put the system call in the package
> to
> | > | have it run when installing the package?
> | >
> | >> You don't. As I said, 'R CMD INSTALL' et all do that.
> | >> Download an existing package with source, install it. Study its sources,
> | >> study the 'Writing R Extensions' manual. Ask on r-devel.
> | >> Basic R questions are off-topic here.
> | >
> | > |>> Would I use the same command and just include it in a file somewhere
> in
> | > the
> | > |>> package?
> | > |>> If so, which file?
> | > |>
> | > |> Hmm ... I'm curious what you're trying to do, exactly?
> | > |
> | > | I'm trying to figure out how take commands such as " R CMD SHLIB X.cc
> | > | X_main
Re: [Rd] FW: [Rcpp-devel] Question on 5.6 Interfacing C++ code
Ah, that's simple, thanks!
On 4/21/11 10:57 AM, "Simon Urbanek" wrote:
>
> On Apr 21, 2011, at 10:52 AM, Sean Robert McGuffee wrote:
>
>> Thanks,
>> That's great, but I don't know how to determine what foo is.
>
> It's the name of your package.
>
>
>> How do I declare the name of the package?
>>
>
> in DESCRIPTION:
> Package: name
>
> and the directory of your package has to have the same name - please do read
> http://r.research.att.com/man/R-exts.html#Creating-R-packages
>
> Cheers,
> Simon
>
>
>>
>> On 4/21/11 7:16 AM, "Duncan Murdoch" wrote:
>>
>>> On 11-04-20 11:33 AM, Sean Robert McGuffee wrote:
Hi, apparently I sent my question about using R and C++ to the wrong list,
ironically seeing as that list was called Rcpp. Anyway, I was directed to
post my question here. To summarize my current question, I have found two
commands that I want to be able to put into a package. The commands are 'R
CMD SHLIB X.cc X_main.cc' and
'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),' which I would like to
run when my package is installed and maybe have the second command run
again
when my package is to be used. I've been trying to figure out the
documentation and learn through examples, but I'm just not getting it and
have been trying for weeks.
Does anyone on this site have any suggestions for me?
>>>
>>> Assuming those lines work on their own, just do the following:
>>>
>>> 1. Put those *.cc files into the src directory of your package. (You
>>> may need to create it.)
>>>
>>> 2. Put useDynLib(foo) into the NAMESPACE file of your foo package.
>>>
>>> 3. Call those functions using .C("X", args, PACKAGE="foo").
>>>
>>> That's it.
>>>
>>> Duncan Murdoch
>>>
Thanks, Sean
|On 20 April 2011 at 10:20, Sean Robert McGuffee wrote:
|
|
| Hi, thanks!
|
|>On 4/20/11 10:03 AM, "Steve Lianoglou"
wrote:
|> Hi,
|>
|> On Wed, Apr 20, 2011 at 9:49 AM, Sean Robert McGuffee
|>wrote:
|>> Hi, I have a quick couple of questions about some of the documentation
on
|>> the web page:
|>>
http://cran.r-project.org/doc/manuals/R-exts.html#Linking-GUIs-and-other-fr
o
n
|>> t_002dends-to-R
|>> under the heading:
|>> 5.6 Interfacing C++ code
|>>
|>> Question 1:
|>> If I¹m at a terminal, I can type the instructions they suggest:
|>> R CMD SHLIB X.cc X_main.cc
|>> If I wanted a package to do this, how would I tell the package to do
that
|>> same thing?
|>
|> Just to make sure we're all on the same page, you want an R package to
|> compile some source code into a shared library/dll from inside R?
|>
|> Not sure if there's a "baked in" way for that to happen, but maybe you
|> can invoke `R CMD WHATEVER` from inside R using the `system` function:
|>
|> R> ?system
|>
|
| ok, so where in the package would I put the system call in the package to
| have it run when installing the package?
> You don't. As I said, 'R CMD INSTALL' et all do that.
> Download an existing package with source, install it. Study its sources,
> study the 'Writing R Extensions' manual. Ask on r-devel.
> Basic R questions are off-topic here.
|>> Would I use the same command and just include it in a file somewhere
in
the
|>> package?
|>> If so, which file?
|>
|> Hmm ... I'm curious what you're trying to do, exactly?
|
| I'm trying to figure out how take commands such as " R CMD SHLIB X.cc
| X_main.cc" followed by "dyn.load(paste("X", .Platform$dynlib.ext, sep =
| ""))," which are commands I can get to work for myself as a human
| interactively, and put the commands into a package to be automatically
run
| when installing the package. I mean, it's great if I can compile a c++
file
| and then use it inside R, but I'm only doing that so I can let other
people
| do that via a package. As much as I read this documentation, I keep
missing
> Again, I like working from an existing, working package. As I said, there
> are
> almost 1000 to pick from.
> Please direct follow-ups that have no bearing on Rcpp to r-devel.
> Dirk
I've tried to figure this out for weeks by looking at other packages and
reading the confusing and nonintegrated documentation, but it hasn't taught
me how to put the two commands into a package so that they are run when the
package is installed. I'm simply trying to find out where in my package I
should put the commands 'R CMD SHLIB X.cc X_main.cc' and
'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),'
in order to have them run when my package is installed.
| the connections between the different sections. This is a section I am
| loving bec
Re: [Rd] FW: [Rcpp-devel] Question on 5.6 Interfacing C++ code
Please, please, please read the documentation before sending more
questions to the list. You also have the source code, so you can look
at what "R CMD build" and "R CMD INSTALL" are doing.
--
Joshua Ulrich | FOSS Trading: www.fosstrading.com
On Thu, Apr 21, 2011 at 10:16 AM, Sean Robert McGuffee
wrote:
>
> So, how is the package turning it's name into those commands?
> Does the installation automatically list the src directory and iteratively
> run a loop over each file and call 'R CMD SHLIB objectOfIterator' ?
> The reason this is so important is because itšs easy to get things to work
> via a terminal command 'R CMD SHLIB someSourceFile.cppš, so I want to be
> able to take things that work that way and put them inside a package. It
> seems peculiar to me that R needs to access functions through a C wrapper
> too. Išm not sure why it canšt access C++ functions directly. What R is
> doing is over my head because it is calling functions that were not compiled
> into it. I mean, if I want to call a C or C++ function from C++ code, I have
> to convince my compiler that I have a header and all definitions behind the
> declarations in my source files to compile my own programs. I donšt know how
> R works when the program is compiled way in advance and is then somehow
> calling on declarations made later in another place. I think objective C/C++
> allows for this type of thing where you can write code to call something
> that is declared but not yet defined. However, Išm not sure what R is doing?
> Is R doing the same thing a compiler would do and creating itšs own binary
> instructions for the launch of a function, or is it creating a new
> executable and launching that as itšs own application and then somehow
> communicating with it?
> Sean
>
>
> On 4/21/11 7:52 AM, "Dirk Eddelbuettel" wrote:
>
>>
>> On 21 April 2011 at 07:16, Duncan Murdoch wrote:
>> | On 11-04-20 11:33 AM, Sean Robert McGuffee wrote:
>> | > Hi, apparently I sent my question about using R and C++ to the wrong
>> list,
>> | > ironically seeing as that list was called Rcpp. Anyway, I was directed to
>> | > post my question here. To summarize my current question, I have found two
>> | > commands that I want to be able to put into a package. The commands are
>> 'R
>> | > CMD SHLIB X.cc X_main.cc' and
>> | > 'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),' which I would like to
>> | > run when my package is installed and maybe have the second command run
>> again
>> | > when my package is to be used. I've been trying to figure out the
>> | > documentation and learn through examples, but I'm just not getting it and
>> | > have been trying for weeks.
>> | > Does anyone on this site have any suggestions for me?
>> |
>> | Assuming those lines work on their own, just do the following:
>> |
>> | 1. Put those *.cc files into the src directory of your package. (You
>> | may need to create it.)
>> |
>> | 2. Put useDynLib(foo) into the NAMESPACE file of your foo package.
>> |
>> | 3. Call those functions using .C("X", args, PACKAGE="foo").
>> |
>> | That's it.
>>
>> We told Sean this twice or three times already over in this thread
>>
>> http://thread.gmane.org/gmane.comp.lang.r.rcpp/1808
>>
>> but the message does not seem to sink in. He keeps asking where to put 'R
>> CMD SHLIB' and doesn't seem to hear when we say there is none in a package...
>>
>> Dirk
>>
>> | Duncan Murdoch
>> |
>> | > Thanks, Sean
>> | >
>> | > |On 20 April 2011 at 10:20, Sean Robert McGuffee wrote:
>> | > |
>> | > |
>> | > | Hi, thanks!
>> | > |
>> | > |>On 4/20/11 10:03 AM, "Steve Lianoglou"
>> | > wrote:
>> | > |> Hi,
>> | > |>
>> | > |> On Wed, Apr 20, 2011 at 9:49 AM, Sean Robert McGuffee
>> | > |> wrote:
>> | > |>> Hi, I have a quick couple of questions about some of the
>> documentation
>> | > on
>> | > |>> the web page:
>> | > |>>
>> | >
>> http://cran.r-project.org/doc/manuals/R-exts.html#Linking-GUIs-and-other-fro
>> | > n
>> | > |>> t_002dends-to-R
>> | > |>> under the heading:
>> | > |>> 5.6 Interfacing C++ code
>> | > |>>
>> | > |>> Question 1:
>> | > |>> If Išm at a terminal, I can type the instructions they suggest:
>> | > |>> R CMD SHLIB X.cc X_main.cc
>> | > |>> If I wanted a package to do this, how would I tell the package to do
>> | > that
>> | > |>> same thing?
>> | > |>
>> | > |> Just to make sure we're all on the same page, you want an R package
>> to
>> | > |> compile some source code into a shared library/dll from inside R?
>> | > |>
>> | > |> Not sure if there's a "baked in" way for that to happen, but maybe
>> you
>> | > |> can invoke `R CMD WHATEVER` from inside R using the `system`
>> function:
>> | > |>
>> | > |> R> ?system
>> | > |>
>> | > |
>> | > | ok, so where in the package would I put the system call in the package
>> to
>> | > | have it run when installing the package?
>> | >
>> | >> You don't. As I said, 'R CMD INSTALL' et all do that.
>> | >> Download an existing package with source, install it. Study
Re: [Rd] FW: [Rcpp-devel] Question on 5.6 Interfacing C++ code
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
what they do to c or c++ commands that I might understand:
R-2.13.0/src/:$grep '"INSTALL"' */*/*/*
library/tools/R/check.R:args <- c("INSTALL", "-l",
shQuote(libdir), INSTALL_opts,
library/tools/R/install.R: "INSTALL", "--no-multiarch")
library/tools/R/install.R: "INSTALL",
"--no-multiarch")
library/utils/R/packages2.R:if(!file.exists(file.path(R.home("bin"),
"INSTALL")))
in a c file that does recognize install, it runs a separate command, and I
have no idea how to trace that command to a c or c++ source code:
if (!strcmp(argv[cmdarg], "INSTALL")) {
snprintf(cmd, CMD_LEN,
"%s/%s/Rterm.exe -e tools:::.install_packages() R_DEFAULT_PACKAGES=
LC_COLLATE=C --no-restore --slave --args ",
getRHOME(3), BINDIR);
PROCESS_CMD("nextArg");
}
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
On 4/21/11 11:21 AM, "Joshua Ulrich" wrote:
> Please, please, please read the documentation before sending more
> questions to the list. You also have the source code, so you can look
> at what "R CMD build" and "R CMD INSTALL" are doing.
> --
> Joshua Ulrich | FOSS Trading: www.fosstrading.com
>
>
>
> On Thu, Apr 21, 2011 at 10:16 AM, Sean Robert McGuffee
> wrote:
>>
>> So, how is the package turning it's name into those commands?
>> Does the installation automatically list the src directory and iteratively
>> run a loop over each file and call 'R CMD SHLIB objectOfIterator' ?
>> The reason this is so important is because itšs easy to get things to work
>> via a terminal command 'R CMD SHLIB someSourceFile.cppš, so I want to be
>> able to take things that work that way and put them inside a package. It
>> seems peculiar to me that R needs to access functions through a C wrapper
>> too. Išm not sure why it canšt access C++ functions directly. What R is
>> doing is over my head because it is calling functions that were not compiled
>> into it. I mean, if I want to call a C or C++ function from C++ code, I have
>> to convince my compiler that I have a header and all definitions behind the
>> declarations in my source files to compile my own programs. I donšt know how
>> R works when the program is compiled way in advance and is then somehow
>> calling on declarations made later in another place. I think objective C/C++
>> allows for this type of thing where you can write code to call something
>> that is declared but not yet defined. However, Išm not sure what R is doing?
>> Is R doing the same thing a compiler would do and creating itšs own binary
>> instructions for the launch of a function, or is it creating a new
>> executable and launching that as itšs own application and then somehow
>> communicating with it?
>> Sean
>>
>>
>> On 4/21/11 7:52 AM, "Dirk Eddelbuettel" wrote:
>>
>>>
>>> On 21 April 2011 at 07:16, Duncan Murdoch wrote:
>>> | On 11-04-20 11:33 AM, Sean Robert McGuffee wrote:
>>> | > Hi, apparently I sent my question about using R and C++ to the wrong
>>> list,
>>> | > ironically seeing as that list was called Rcpp. Anyway, I was directed
>>> to
>>> | > post my question here. To summarize my current question, I have found
>>> two
>>> | > commands that I want to be able to put into a package. The commands are
>>> 'R
>>> | > CMD SHLIB X.cc X_main.cc' and
>>> | > 'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),' which I would like
>>> to
>>> | > run when my package is installed and maybe have the second command run
>>> again
>>> | > when my package is to be used. I've been trying to figure out the
>>> | > documentation and learn through examples, but I'm just not getting it
>>> and
>>> | > have been trying for weeks.
>>> | > Does anyone on this site have any suggestions for me?
>>> |
>>> | Assuming those lines work on their own, just do the following:
>>> |
>>> | 1. Put those *.cc files into the src directory of your package. (You
>>> | may need to create it.)
>>> |
>>> | 2. Put useDynLib(foo) into the NAMESPACE file of your foo package.
>>> |
>>> | 3. Call those functions using .C("X", args, PACKAGE="foo").
>>> |
>>> | That's it.
>>>
>>> We told Sean this twice or three times already over in this thread
>>>
>>> http://thread.gmane.org/gmane.comp.lang.r.rcpp/1808
>>>
>>> but the message does not seem to sink in. He keeps asking where to put 'R
>>> CMD SHLIB' and doesn't seem to hear when we say there is none in a
>>> package...
>>>
>>> Dirk
>>>
>>> | Duncan Murdoch
>>> |
>>> | > Thanks, Sean
>>> | >
>>> | > |On 20 April 2011 at 10:20, Sean Robert McGuffee wrote:
>>> | > |
>>> | > |
>>> | > | Hi, thanks!
>>> | > |
>>> | > |>On 4/20/
Re: [Rd] How to get R to compile with PNG support
Thanks for all the feedback. First, our update, then two responses. >From Jason Grout: +++ I finally got it working. After mucking around in the R configure file a bit and trying out some of the different tests, as well as comparing a working system with our broken system, I realized that `pkg-config --exists pangocairo` was working on the good system and not working on the broken system. So I installed libpango1.0-dev, and now R picks up the cairo package, which in turn means that my capabilities is now: > capabilities() jpeg png tifftcltk X11 aqua http/ftp sockets TRUE TRUEFALSEFALSEFALSEFALSE TRUE TRUE libxml fifo clediticonv NLS profmemcairo TRUE TRUE TRUE TRUE TRUEFALSE TRUE So in short, I think what I did was install libcairo-dev and libpango1.0-dev. There might have been other stuff in there that was needed; I'm not sure. When I build a new system again, I'll try just installing those packages and see if it is sufficient. For the record, I had also installed xorg-dev as well. +++ My comment: As someone who didn't know what configure scripts were a couple years ago, this is maddening; I don't see anything about libpango or whatever in the FAQs. Luckily, Jason knows a lot more than I do! @Dirk: > | Note that we have installed the cairo devel package on this very > | machine, but it's not being picked up - maybe it's looking in the > | wrong place? That is one of the reasons this is confusing. > > You have to understand that even though this problem may seem urgent and > novel to you and the Sage team, Novel, yes; urgent only to us, certainly we don't assume it's urgent to you :) > it is actually about as old as the web and R > itself. In a nutshell, we all (in the people reading r-help and r-devel > sense) have been explaining to folks since the late 1990s that in order to > run png() to 'just create some charts for a webserver' ... you need an X11 > server because that is where the font metrics come from. Or else no png for It's true this is findable, but the difference between having X11 on the system and having the display is arcane for those who just want to use R. But I understand your point. > is life. System such as Sage become so large because having things like this > around on all deployment systems implies (at least to some degree) > replicating fundamental OS level features because they unfortunately have > supply things missing or broken across OSs. Yes, that is true. We know of many people who download Sage because it's the easiest way to install Z, where Z is some specific mathematical program that is impossible to configure properly without special knowledge. Or, until fairly recently, to get Cython. @Simon: That's new to me that X11 is installed by default now, but it looks like you are right. However, we don't rely on this for Mac; we make sure to configure for quartz when we build - which I assume is separate from the other stuff? But updating the FAQ about this would be really great for future users :) Also thanks for the hint on all the other (possibly) needed stuff. Yikes! AFAIK this is an Ubuntu machine we're talking about. To all - if we come up with any more reliable way to make this work universally, i.e. with *exact* instructions for what to download, we will definitely pass that upstream. Thank you. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Sweave support added to rgl package
I've just committed some changes to rgl that will probably detect bitmaps that are specified to be too large. As well, Brian Ripley backported some of the R-devel additions to the RweaveLatex driver, so now R 2.13.0-patched (revision 55572 or newer) should work as well as R-devel. Duncan Murdoch On 20/04/2011 8:56 PM, Duncan Murdoch wrote: On 20/04/2011 7:10 PM, Dominick Samperi wrote: > On Wed, Apr 20, 2011 at 2:29 PM, Duncan Murdoch > wrote: >> On 20/04/2011 1:52 PM, Dominick Samperi wrote: >>> >>> On Tue, Apr 19, 2011 at 2:18 PM, Duncan Murdoch >>> 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: <>= 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. <>= 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 >>> >>> I inserted your example into testrgl.Rnw under R 2.13.0, with >>> Sweave.snapshot() >>> at the end of both chunks, but things did not work as expected. >>> >>> I used: >>> $ R CMD Sweave testrgl.Rnw >>> $ pdflatex tesetrgl >>> (view testrgl.pdf) >>> >>> When R CMD Sweave is run the graphics is displayed interactively. >> >> That's unavoidable as far as I know. I don't think there's a general >> purpose way to tell OpenGL to render in the background, so it works by >> rendering on screen, then copying a bitmap to the .png file. >>> >>> There is no graphics in the PDF file, even though both .png files >>> are read when pdflatex is run. >> >> Do they look okay? One possible problem is that you may have asked for a >> bitmap too big for your hardware to render, in which case those png files >> will end up with junk (probably blank). Setting resolution=100 in the chunk >> headers will do it more coarsely. (The default is 300 dpi.) The same >> effect comes from width=1, height=1 (or some other small numbers). >> >> Duncan Murdoch >> > > The resolution=100 tip fixed the problem, thanks. I'll see if I am skipping over some error message in there. It would be much better for Sweave to fail with an error than generate empty images. > Now I see the snapshots > in the PDF file. Using this in a package will certainly change the > user experience, > but it moves away from the traditional batch-oriented R package > processing, it seems to me. I don't follow that. > The idea of adding support for movies and 3D graphics to Sweave/PDF files > sounds very interesting and revolutionary. Movies will likely be pretty slow. I think you'll want caching of some sort if you want to produce those. Duncan Murdoch > > Dominick __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] problem subsetting of a reference class
I am trying to define subset operator for a reference class and hitting some
problem i am unable to diagnose.To give an example, here is a toy class
generator that is a wrapper around a list
tmpGEN<-setRefClass("TMP", fields=list(
namelist="list"
))
tmpGEN$methods('add'=function(obj, name){
namelist[[name]]<<-obj
})
tmpGEN$methods('['=function(name){
if(class(name)!="character")
stop('to return cache element need to pass its
name')
ind<-match(name, names(namelist))
if(is.na(ind))
stop('data to remove is not in namelist')
namelist[[name]]
})
==
when i try to use it, the following happens
v<-rnorm(10)
tmp<-tmpGEN$new()
tmp$add(v, 'random')
. up until here everything is ok, class is generated and vector is
added. Now when i do
tmp['random']
i get error message
Error in tmp["random"] : object of type 'S4' is not subsettable
Not sure if it means that i cannot define "[" operator for a class or if i
am doing it syntactically wrong
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Re: [Rd] problem subsetting of a reference class
You're confusing functional and OOP-style methods.
Since you define an OOP-style method, you need to invoke it in OOP style.
With your example:
> tmp$`[`("random")
[1] -1.439131143 -0.630354726 0.822006263 -0.651707539 0.475332681
[6] 0.002680224 1.539035675 -0.117609566 2.066227300 1.111270997
>
You could if you wanted define a functional method via setMethod() to
allow functional access, by invoking the $`[`() method--preferably after
changing its name. It's probably a matter of opinion whether that's a
good use of OOP-style methods.
On 4/21/11 12:24 PM, A Zege wrote:
I am trying to define subset operator for a reference class and hitting some
problem i am unable to diagnose.To give an example, here is a toy class
generator that is a wrapper around a list
tmpGEN<-setRefClass("TMP", fields=list(
namelist="list"
))
tmpGEN$methods('add'=function(obj, name){
namelist[[name]]<<-obj
})
tmpGEN$methods('['=function(name){
if(class(name)!="character")
stop('to return cache element need to pass its
name')
ind<-match(name, names(namelist))
if(is.na(ind))
stop('data to remove is not in namelist')
namelist[[name]]
})
==
when i try to use it, the following happens
v<-rnorm(10)
tmp<-tmpGEN$new()
tmp$add(v, 'random')
. up until here everything is ok, class is generated and vector is
added. Now when i do
tmp['random']
i get error message
Error in tmp["random"] : object of type 'S4' is not subsettable
Not sure if it means that i cannot define "[" operator for a class or if i
am doing it syntactically wrong
--
View this message in context:
http://r.789695.n4.nabble.com/problem-subsetting-of-a-reference-class-tp3466690p3466690.html
Sent from the R devel mailing list archive at Nabble.com.
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__
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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
