[Rd] problem with Rcmdr Plugins

[Hodgess, Erin]

Dear R Development People:

I have written a couple of plugins for Rcmdr and they do not seem to work with 
R-2.11.0.

Here is the output:
> library(RcmdrPlugin.epack)
Loading required package: Rcmdr
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: car
--- Please select a CRAN mirror for use in this session ---

Rcmdr Version 1.5-4


Attaching package: 'Rcmdr'

The following object(s) are masked from 'package:tcltk':

tclvalue

Loading required package: rgl
Loading required package: TeachingDemos
Loading required package: tseries
Loading required package: quadprog
Loading required package: zoo

'tseries' version: 0.10-22

'tseries' is a package for time series analysis and computational
finance.

See 'library(help="tseries")' for details.

Loading required package: abind
Loading required package: MASS
Error : package 'rgl' is required by 'RcmdrPlugin.epack' so will not be detached
Error in library(RcmdrPlugin.epack) : 
  .First.lib failed for 'RcmdrPlugin.epack'
> 

This is on a Windows XP.  I'm downloading the Rcmdr requirements on a Linux 
machine as we speak.

Have you run into this please?
Thanks,
Erin


Erin M. Hodgess, PhD
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodge...@uhd.edu


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[Rd] a side note to the Rcmdr issue

[Hodgess, Erin]

Hi again.

On Windows, when I try to use the "install packages" from the menu, there is no 
Rcmdr and no RcmdrPlugins to be seen.

thanks,
Erin


Erin M. Hodgess, PhD
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodge...@uhd.edu


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[Rd] accessing underlying code

[Hodgess, Erin]

Dear R Developers:

Is there a way to look at the underlying code from such items as 
R_setup_starma, please?

Thanks,
Erin


Erin M. Hodgess, PhD
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodge...@uhd.edu


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[Rd] using svd in regression with arima

[Hodgess, Erin]

Dear R Developers:

Why is it that the singular value decomposition is used when running regression 
with arima, please?  I've been looking for a reference for that but have come 
up empty so far.

Thank you for any help.

Sincerely,
Erin


Erin M. Hodgess, PhD
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodge...@uhd.edu


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Re: [Rd] R 2.12.0 doesn't install properly under Windows Vista

[Hodgess, Erin]

Dear R Developers:
 
I'm having the same trouble (no Rgui.exe) when compiling from source.
 
This is on a Windows XP with the latest Rtools.
 
Sorry to be a pest.
Thanks,
Erin
 
 
Erin M. Hodgess, PhD
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodge...@uhd.edu
 



From: r-devel-boun...@r-project.org on behalf of Duncan Murdoch
Sent: Sat 10/16/2010 6:01 PM
To: Dominick Samperi
Cc: r-devel@r-project.org
Subject: Re: [Rd] R 2.12.0 doesn't install properly under Windows Vista



On 16/10/2010 4:55 PM, Dominick Samperi wrote:
> After installing R 2.12.0 under windows Vista it does not start because it
> cannot
> find Rgui.exe. Indeed, the contents of R\R-2.12.0\bin are:
>
> config.sh
> R.exe
> Rscript.exe
> Sd2Rd.pl
>
> It appears that a few things are missing...

The original build was missing the contents of bin/i386, which is where
32 bit binaries are stored now.  A new build has been done, and it will
eventually make it to CRAN and the mirrors.

Check the date on the bottom of the bin/windows/base page on CRAN:
2010-10-15 is bad, 2010-10-16 is good (as far as I know).

Duncan Murdoch

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Re: [Rd] R 2.12.0 problems with Windows XP 32-bit binary installer

[Hodgess, Erin]

I found the Rgui.exe under directory R\R-2.12.0\bin\i386.
 
Thanks,
Erin
 
 
Erin M. Hodgess, PhD
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodge...@uhd.edu
 



From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Sent: Sun 10/17/2010 7:53 PM
To: bill.venab...@csiro.au
Cc: Hodgess, Erin; r-devel@r-project.org
Subject: Re: R 2.12.0 problems with Windows XP 32-bit binary installer



bill.venab...@csiro.au wrote:
> I am having a problem with the installed R 2.12.0 on 32-bit Windows XP 
> machine using the binary version.
>
> The installer I am using is R-2.12.0-win.exe .  The problem I have is that 
> some of my installed packages will not load, in particular PolynomF, which 
> has a pre-compiled .dll.  Other packages such as SOAR, which is pure R, 
> attach and work without a hitch.
>
> The error message I am getting when trying to load PolynomF is a question 
> whether or not the package has been compiled for the present architecture.  
> (This package works without a hitch on R-2.11.1, for example.)
>
> Is there any significance in the name of the installer now including just 
> "win" rather than "win32", as it was in the last release?
>
> Is it the case that all packages will have to be re-built for the present 
> release?


Generally packages do need to be rebuilt for new versions of R (other
than patch releases, where only the last digit changes).  R 2.12.0
supports both 32 bit and 64 bit Windows in the same installation, and
since Windows doesn't have MacOS-like "universal" binaries, that means
binaries need to be put in the right place.  Generally that's an i386
subdirectory for 32 bit, and an x64 directory for 64 bit.

I don't know why a 32 bit DLL wouldn't work with 32 bit R 2.12.0, but if
it was installed for 2.11.1, it might not be in the right place.

Duncan Murdoch



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[Rd] problem with building bitmapdll on Windows

[Hodgess, Erin]

Dear R Development People:
 
I was trying to build R-2.12.2 from source on a Windows XP machine.
 
Doing the make all recommended works fine, but building the bitmap dll is a 
problem.
 
It seems to be in the libpng directory.  I got libpng-1.5.1, and untarred it.  
However, there is no makefile.mingw file in the scripts directory.
 
I then obtained a version of libpng-1.4.5, and the file is there.  The dll file 
builds fine.
 
We might want to look at the libpng-1.5.1 directory.
 
Thanks for listening,
Sincerely,
Erin
 
 
Erin M. Hodgess, PhD
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodge...@uhd.edu
 

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Re: [Rd] problem with building bitmapdll on Windows

[Hodgess, Erin]

Sorry about that.
 
 
 
Erin M. Hodgess, PhD
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodge...@uhd.edu
 



From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk]
Sent: Sat 3/5/2011 12:00 PM
To: Hodgess, Erin
Cc: r-devel@r-project.org
Subject: Re: [Rd] problem with building bitmapdll on Windows



On Sat, 5 Mar 2011, Hodgess, Erin wrote:

> Dear R Development People:
>
> I was trying to build R-2.12.2 from source on a Windows XP machine.
>
> Doing the make all recommended works fine, but building the bitmap
> dll is a problem.
>
> It seems to be in the libpng directory.  I got libpng-1.5.1, and
> untarred it.  However, there is no makefile.mingw file in the
> scripts directory.
>
> I then obtained a version of libpng-1.4.5, and the file is there.
> The dll file builds fine.
>
> We might want to look at the libpng-1.5.1 directory.

libpng 1.5.1 is not supported for R 2.12.2: it will be for 2.13.0.
The documentation does say so ...

You need libpng, jpeg and libtiff sources (available, e.g., from
http://www.libpng.org/, http://www.ijg.org <http://www.ijg.org/>  and
ftp://ftp.remotesensing.org/pub/libtiff/). You will need files
libpng-1.2.18.tar.gz (including ?1.4.x' but not ?1.5.x'),
jpegsrc.v6b.tar.gz, tiff-3.8.0.tar.gz (but not ?4.0.0beta') or later.

>
> Thanks for listening,
> Sincerely,
> Erin
>
>
> Erin M. Hodgess, PhD
> Associate Professor
> Department of Computer and Mathematical Sciences
> University of Houston - Downtown
> mailto: hodge...@uhd.edu
>
>
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>
> __
> 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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[Rd] a quick question before I proceed

[Hodgess, Erin]

Is this the proper forum for questions on Fortran, MPI, RInside, and Rcpp, 
please?

Thanks,
Erin


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[Rd] strange behavior for RcmdrPlugin.qual

[Hodgess, Erin]

Hello!

Over the weekend, I updated my RcmdrPlugin.qual package.

It works fine on a 64 bit Windows machine but not a 32 bit.  This is very 
strange.  The new menu with all of the Quality Control stuff does not appear.

Have any of you run into this sort of thing before, please?

Thanks,
Sincerely,
Erin


Erin M. Hodgess, Ph.D.
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodge...@uhd.edu


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Re: [Rd] Looking for new maintainer of orphans R2HTML SemiPar cghseg hexbin lgtdl monreg muhaz operators pamr

[Hodgess, Erin]

I'll do R2HTML, please.

Thanks,
Erin


From: r-devel-boun...@r-project.org [r-devel-boun...@r-project.org] on behalf 
of Uwe Ligges [lig...@statistik.tu-dortmund.de]
Sent: Tuesday, September 09, 2014 8:53 AM
To: Luca Sartore
Cc: c...@r-project.org; R-Devel
Subject: Re: [Rd] Looking for new maintainer of orphans R2HTML SemiPar cghseg 
hexbin lgtdl monreg muhaz operators pamr

On 09.09.2014 09:52, Luca Sartore wrote:
> Dear all,
>
> I will pick up monreg.

Please try to coordinate efforts with Scott Kostyshak  who offered the
same thing yesterday.

Best,
Uwe Ligges



> Best regards,
> Luca Sartore
>
>
> 2014-09-08 1:03 GMT+02:00 Uwe Ligges :
>>
>>
>> On 08.09.2014 01:01, Gregory R. Warnes wrote:
>>>
>>> And I’ll pick up hexbin.
>>
>>
>> Err, that one has been adopted a month ago already.
>>
>> open are:
>>
>> SemiPar cghseg monreg
>>
>>
>> Best,
>> Uwe Ligges
>>
>>
>>>
>>> -Greg
>>>
>>> On Sep 7, 2014, at 12:17 PM, Romain Francois 
>>> wrote:
>>>
 I'll pick up operators.

 Le 7 sept. 2014 à 18:03, Uwe Ligges  a
 écrit :

>
>
> On 05.09.2014 20:25, Greg Snow wrote:
>>
>> Uwe,
>>
>> Have all of these packages found new maintainers? if not, which ones
>> are still looking to be adopted?
>
>
> Thanks for asking, the ones still looking to be adaopted are:
> SemiPar cghseg monreg operators
>
> Best,
> Uwe Ligges
>
>
>>
>> thanks,
>>
>> On Fri, Aug 8, 2014 at 10:41 AM, Uwe Ligges 
>> wrote:
>>>
>>> Dear maintainers and R-devel,
>>>
>>> Several orphaned CRAN packages are about to be archived due to
>>> outstanding
>>> QC problems, but have CRAN and BioC packages depending on them which
>>> would
>>> be broken by the archival (and hence need archiving alongside).
>>> Therefore we are looking for new maintainers taking over
>>> maintainership for
>>> one or more of the following packages:
>>>
>>> R2HTML SemiPar cghseg hexbin lgtdl monreg muhaz operators pamr
>>>
>>> Package maintainers whose packages depend on one of these may be
>>> natural
>>> candidates to become new maintainers.
>>> Hence this messages is addressed to all these maintainers via BCC and
>>> to
>>> R-devel.
>>>
>>> See
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> for information on the QC issues and the reverse dependencies.
>>>
>>> Best wishes,
>>> Uwe Ligges
>>> (for the CRAN team)
>>>
>>> __
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>>
>>
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


 __
 R-devel@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>>
>>
>> __
>> 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
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[Rd] trouble compiling R-patched from source on Windows 64 bit

[Hodgess, Erin]

Hello!

I'm trying to install R-patched from source on a Windows 64 bit laptop.

I have installed R-tools 2.16 and set up the jpeg, tiff, and libpng files 

Here is the output:

c:\R64\R-patched\src\gnuwin32>make all recommended
make all recommended
make[1]: `MkRules' is up to date.
make[4]: Nothing to be done for `svnonly'.
installing C headers
make[2]: Nothing to be done for `all'.
make[2]: `libRblas.dll.a' is up to date.
make[5]: Nothing to be done for `svnonly'.
installing C headers
make --no-print-directory -C ../extra/intl CFLAGS='-O3 -Wall -pedantic 
-mtune=core2' -f Makefile.win
make --no-print-directory -C ../appl CFLAGS='-O3 -Wall -pedantic -mtune=core2' 
FFLAGS='-O3 -mtune=core2' -f Makefile.win
make --no-print-directory -C ../nmath CFLAGS='-O3 -Wall -pedantic -mtune=core2' 
FFLAGS='-O3 -mtune=core2' -f Makefile.win
make --no-print-directory -C ../main CFLAGS='-O3 -Wall -pedantic -mtune=core2' 
FFLAGS='-O3 -mtune=core2' malloc-DEFS='-DLEA_MALLOC' -f Makefile.win
make --no-print-directory -C ./getline CFLAGS='-O3 -Wall -pedantic -mtune=core2'
make[4]: `gl.a' is up to date.
make -f Makefile.win makeMakedeps
make -f Makefile.win libpcre.a
make[5]: `libpcre.a' is up to date.
make[4]: Nothing to be done for `all'.
make -f Makefile.win makeMakedeps
make -f Makefile.win libtre.a
make[5]: `libtre.a' is up to date.
make[4]: Nothing to be done for `all'.
make[5]: `stamp' is up to date.
make[5]: `liblzma.a' is up to date.
x86_64-w64-mingw32-gcc -std=gnu99  -shared -s -mwindows -o R.dll R.def 
console.o dataentry.o dynload.o edit.o editor.o embeddedR.o extra.o opt.o 
pager.o preferences.o psignal.o rhome.o rt_complete.o rui.o run.o shext.o 
sys-win32.o system.o dos_wglob.o malloc.o ../main/libmain.a ../appl/libappl.a 
../nmath/libnmath.a getline/gl.a ../extra/xdr/libxdr.a ../extra/pcre/libpcre.a 
../extra/bzip2/libbz2.a ../extra/intl/libintl.a ../extra/trio/libtrio.a 
../extra/tzone/libtz.a ../extra/tre/libtre.a ../extra/xz/liblzma.a dllversion.o 
 -L. -lgfortran -lRblas -L../../bin/x64 -lRzlib -lRgraphapp -lRiconv -lcomctl32 
-lversion  
c:/rtools/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.5.2/../../../../x86_64-w64-mingw32/bin/ld.exe:
 skipping incompatible ./libRblas.dll.a when searching for -lRblas
c:/rtools/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.5.2/../../../../x86_64-w64-mingw32/bin/ld.exe:
 skipping incompatible ./libRblas.dll.a when searching for -lRblas
c:/rtools/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.5.2/../../../../x86_64-w64-mingw32/bin/ld.exe:
 cannot find -lRblas
collect2: ld returned 1 exit status
make[3]: *** [R.dll] Error 1
make[2]: *** [../../bin/x64/R.dll] Error 2
make[1]: *** [rbuild] Error 2
make: *** [all] Error 2

c:\R64\R-patched\src\gnuwin32>

Does this make sense, please?

Thanks in advance for any help.

Sincerely,
Erin



Erin M. Hodgess, PhD
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodge...@uhd.edu


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[Rd] read.pnm question in R-beta

[Hodgess, Erin]

In R-beta (Masked Marvel), when I do the example from the read.pnm help file, 
this is what happens:

x <- read.pnm(system.file("pictures/logo.pgm",package="pixmap")[1])
Warning message:

In rep(cellres, length=2): x is NULL so the result will be NULL
In R-2.15.3, it's all right.

Thanks,
Erin

Erin M. Hodgess, Ph.D.
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodge...@uhd.edu


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[Rd] question about Makeconf and nvcc/CUDA

[Hodgess, Erin]

Dear R development:



I'm not sure if this is the appropriate list, but it's a start.



I would like to put together a package which contains a CUDA program on Windows 
7.  I believe that it has to do with the Makeconf file in the etc directory.



But when I just use the nvcc with the shared option, I can use the dyn.load 
command, but when I use the is.loaded function, it shows FALSE.







Here are the results of the check command:



c:\PROGRA~1\R\R-3.0.1\bin\i386>R CMD check cudasize
R CMD check cudasize
* using log directory 'c:/PROGRA~1/R/R-3.0.1/bin/i386/cudasize.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'cudasize/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cudasize' version '1.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'cudasize' can be installed ... ERROR
Installation failed.
See 'c:/PROGRA~1/R/R-3.0.1/bin/i386/cudasize.Rcheck/00install.out' for details.

And the 00install.out file:

* installing *source* package 'cudasize' ...

** libs



*** arch - i386

cygwin warning:
  MS-DOS style path detected: c:/PROGRA~1/R/R-30~1.1/etc/i386/Makeconf
  Preferred POSIX equivalent is: 
/cygdrive/c/PROGRA~1/R/R-30~1.1/etc/i386/Makeconf
  CYGWIN environment variable option "nodosfilewarning" turns off this warning.
  Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
cygwin warning:
  MS-DOS style path detected: c:/PROGRA~1/R/R-30~1.1/etc/i386/Makeconf
  Preferred POSIX equivalent is: 
/cygdrive/c/PROGRA~1/R/R-30~1.1/etc/i386/Makeconf
  CYGWIN environment variable option "nodosfilewarning" turns off this warning.
  Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
make: `symbols.rds' is up to date.
ERROR: compilation failed for package 'cudasize'

* removing 'c:/PROGRA~1/R/R-3.0.1/bin/i386/cudasize.Rcheck/cudasize'



I've been experimenting with the Makeconf file, but to no avail.



Does anyone have any suggestions, please?



Thanks,

Erin



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Re: [Rd] question about Makeconf and nvcc/CUDA

[Hodgess, Erin]

Now let's try again.  I set up the CYGWIN environment command as kindly 
suggested by Prof. Ripley.

Here are my next steps:

R CMD build cudasize
* checking for file 'cudasize/DESCRIPTION' ... OK
* preparing 'cudasize':
* checking DESCRIPTION meta-information ... OK
* cleaning src
Warning: 
C:/Users/erin/AppData/Local/Temp/RtmpOWOS4q/Rbuilda8820822194/cudasize/man/f1.Rd:33:
 unexpected '{'
Warning: 
C:/Users/erin/AppData/Local/Temp/RtmpOWOS4q/Rbuilda8820822194/cudasize/man/f1.Rd:37:
 unexpected '}'
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'cudasize_1.0.tar.gz'


c:\PROGRA~1\R\R-3.0.1\bin\i386>R CMD check cudasize_1.0.tar.gz 
R CMD check cudasize_1.0.tar.gz 
* using log directory 'c:/PROGRA~1/R/R-3.0.1/bin/i386/cudasize.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'cudasize/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cudasize' version '1.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory 'src' contains:
  cuda4.cu
These are unlikely file names for src files.
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'cudasize' can be installed ... ERROR
Installation failed.
See 'c:/PROGRA~1/R/R-3.0.1/bin/i386/cudasize.Rcheck/00install.out' for details.

And the 00install.out file is:
* installing *source* package 'cudasize' ...
** libs

*** arch - i386
ERROR: compilation failed for package 'cudasize'
* removing 'c:/PROGRA~1/R/R-3.0.1/bin/i386/cudasize.Rcheck/cudasize'

So it doesn't seem that CUDA is  working here.  However, if I compile cuda4.cu 
from the command line, it works fine, as seen here:

nvcc -m32 --shared -o cuda4.dll cuda4.cu
 nvcc -m32 --shared -o cuda4.dll cuda4.cu
cuda4.cu
tmpxft_13d4_-5_cuda4.cudafe1.gpu
tmpxft_13d4_-10_cuda4.cudafe2.gpu
cuda4.cu
tmpxft_13d4_-5_cuda4.cudafe1.cpp
tmpxft_13d4_-15_cuda4.ii

So that is my situation.

This is Windows 7, R version 3.0.1
Thanks,
Erin


From: r-devel-boun...@r-project.org [r-devel-boun...@r-project.org] on behalf 
of Prof Brian Ripley [rip...@stats.ox.ac.uk]
Sent: Thursday, July 18, 2013 2:44 AM
To: r-devel@r-project.org
Subject: Re: [Rd] question about Makeconf and nvcc/CUDA

On 18/07/2013 07:45, Hodgess, Erin wrote:
> Dear R development:
>
>
>
> I'm not sure if this is the appropriate list, but it's a start.
>
>
>
> I would like to put together a package which contains a CUDA program on 
> Windows 7.  I believe that it has to do with the Makeconf file in the etc 
> directory.

That message is just that you have not set up Rtools fully.  As it says,
set CYGWIN=nodosfilewarning in your environment.  See §D.3 in the
R-admin manual, e.g.
http://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-command-line-tools
.

We can see nothing from what you supplied, as it was not a build in
clean sources.



>
>
> But when I just use the nvcc with the shared option, I can use the dyn.load 
> command, but when I use the is.loaded function, it shows FALSE.
>
>
>
>
>
>
>
> Here are the results of the check command:
>
>
>
> c:\PROGRA~1\R\R-3.0.1\bin\i386>R CMD check cudasize
> R CMD check cudasize
> * using log directory 'c:/PROGRA~1/R/R-3.0.1/bin/i386/cudasize.Rcheck'
> * using R version 3.0.1 (2013-05-16)
> * using platform: i386-w64-mingw32 (32-bit)
> * using session charset: ISO8859-1
> * checking for file 'cudasize/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'cudasize' version '1.0'
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for executable files ... OK
> * checking for hidden files and directories ... OK
> * checking for portable file names ... OK
> * checking whether package 'cudasize' can be installed ... ERROR
> Installation failed.
> See 'c:/PROGRA~1/R/R-3.0.1/bin/i386/cudasize.Rcheck/00install.out' for 
> details.
>
> And the 00install.out file:
>
> * installing *source* package 'cudasize' ...
>
> ** libs
>
>
>
> *** arch - i386
>
> cygwin warning:
>MS-DOS style path detected: c:/PROGRA~1/R/R-30~1.1/etc/i386

Re: [Rd] question about Makeconf and nvcc/CUDA

[Hodgess, Erin]

Hi again:

Here is another problem that I am having.  Hope this will be the last one.  I 
really want to see if I can put it together.  Sorry for belaboring the issue.

Well, here is my story:

c:\Program Files\R\R-3.0.1\bin\i386>R CMD build cudasize
R CMD build cudasize
* checking for file 'cudasize/DESCRIPTION' ... OK
* preparing 'cudasize':
* checking DESCRIPTION meta-information ... OK
* cleaning src
Warning: 
C:/Users/erin/AppData/Local/Temp/RtmpOKsfga/Rbuild22e066bf13fb/cudasize/man/f1.Rd:33:
 unexpected '{'
Warning: 
C:/Users/erin/AppData/Local/Temp/RtmpOKsfga/Rbuild22e066bf13fb/cudasize/man/f1.Rd:37:
 unexpected '}'
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'cudasize_1.0.tar.gz'


c:\Program Files\R\R-3.0.1\bin\i386>R CMD INSTALL --no-multiarch 
cudasize_1.0.tar.gz 
R CMD INSTALL --no-multiarch cudasize_1.0.tar.gz 
* installing to library 'c:/myRlib'
* installing *source* package 'cudasize' ...
** libs
nvcc -m32 --shared -o cuda4.dll cuda4.cu
cuda4.cu
tmpxft_12fc_-5_cuda4.cudafe1.gpu
tmpxft_12fc_-10_cuda4.cudafe2.gpu
cuda4.cu
tmpxft_12fc_-5_cuda4.cudafe1.cpp
tmpxft_12fc_-15_cuda4.ii
installing to c:/myRlib/cudasize/libs/i386
** R
** preparing package for lazy loading
** help
Warning: 
C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:33:
 unexpected '{'
Warning: 
C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:37:
 unexpected '}'
Warning: 
C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:31:
 All text must be in a section
Warning: 
C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:32:
 All text must be in a section
Warning: 
C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:34:
 All text must be in a section
Warning: 
C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:35:
 All text must be in a section
Warning: 
C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:36:
 All text must be in a section
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (cudasize)

c:\Program Files\R\R-3.0.1\bin\i386>R --vanilla
R --vanilla

R version 3.0.1 (2013-05-16) -- "Good Sport"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(cudasize)
library(cudasize)
> f1
f1
function (x) 
{
y <- .Call("cuda4", as.character(x))
return(y)
}

> f1(2)
f1(2)
Error in .Call("cuda4", as.character(x)) : 
  "cuda4" not resolved from current namespace (cudasize)
Calls: f1 -> .Call
Execution halted

Here is the Makevars.win file

cuda4.dll:
nvcc -m32 --shared -o cuda4.dll cuda4.cu

And finally, the program itself:


#include 
#include 
 
// Kernel that executes on the CUDA device
__global__ void square_array(float *a, int N)
{
  int idx = blockIdx.x * blockDim.x + threadIdx.x;
  if (idx>> (a_d, N);
  // Retrieve result from device and store it in host array
  cudaMemcpy(a_h, a_d, sizeof(float)*N, cudaMemcpyDeviceToHost);
  // Print results
  for (int i=0; i Dear R development:
>
>
>
> I'm not sure if this is the appropriate list, but it's a start.
>
>
>
> I would like to put together a package which contains a CUDA program on 
> Windows 7.  I believe that it has to do with the Makeconf file in the etc 
> directory.
>
>
>
> But when I just use the nvcc with the shared option, I can use the dyn.load 
> command, but when I use the is.loaded function, it shows FALSE.
>
>
>
>
>
>
>
> Here are the results of the check command:
>
>
>
> c:\PROGRA~1\R\R-3.0.1\bin\i386>R CMD check cudasize
> R CMD check cudasize
> * using log directory 'c:/PROGRA~1/R/R-3.0.1/bin/i386/cudasize.Rcheck'
> * using R version 3.0.1 (2013-05-16)
> * using platform: i386-w64-mingw32 (32-bit)
> * using session charset: ISO8859-1
> * checking for file 'cudasize/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'cudasize' version '1.0'
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for executable files ... OK
> * checking for hidden files and directories ... OK
> * checking for portable file names ... OK
> * checking whether package 'cudasize' ca

Re: [Rd] question about Makeconf and nvcc/CUDA

[Hodgess, Erin]

Hi again.

I put in the extern statement.

However, I'm not sure what you mean by changing the signature, please.  

I changed out the routine name from "stuff" to "cuda4" in the cuda4.cu program.

Still getting:

> library(cudasize)
library(cudasize)

> 

> .C("cuda4",as.character(5))
.C("cuda4",as.character(5))
Error in .C("cuda4", as.character(5)) : 
  C symbol name "cuda4" not in load table
Execution halted

c:\Program Files\R\R-3.0.1\bin\i386>

I still want to keep at it.

Thanks so much for all of your help!!!

Erin


From: Duncan Temple Lang [dtemplel...@ucdavis.edu]
Sent: Thursday, July 18, 2013 1:09 PM
To: Hodgess, Erin
Cc: r-devel@r-project.org
Subject: Re: [Rd] question about Makeconf and nvcc/CUDA

Hi Erin

It appears that there is only one file in src that is compile, i.e. cuda4.cu.

That does not contain a routine named cuda4, which is what you are trying to 
invoke
via the .Call("cuda4") expression.

Instead, it contains two routines - one kernel square_array which runs
on the GPU, and the routine stuff.

To be able to call the stuff() routine from R, you would have to
a)  add
  extern "C"
before its definition/declaration so that its name is not mangled by nvcc

b)  change its signature so that it can be invoked via a .Call() or 
alternatively
a .C().

 I would create another routine that acts as an intermediate routine
called from R that then calls stuff().

This assumes that what you showed us of cuda4.cu is all there is in it.
   D.

On 7/18/13 11:01 AM, Hodgess, Erin wrote:
> Hi again:
>
> Here is another problem that I am having.  Hope this will be the last one.  I 
> really want to see if I can put it together.  Sorry for belaboring the issue.
>
> Well, here is my story:
>
> c:\Program Files\R\R-3.0.1\bin\i386>R CMD build cudasize
> R CMD build cudasize
> * checking for file 'cudasize/DESCRIPTION' ... OK
> * preparing 'cudasize':
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> Warning: 
> C:/Users/erin/AppData/Local/Temp/RtmpOKsfga/Rbuild22e066bf13fb/cudasize/man/f1.Rd:33:
>  unexpected '{'
> Warning: 
> C:/Users/erin/AppData/Local/Temp/RtmpOKsfga/Rbuild22e066bf13fb/cudasize/man/f1.Rd:37:
>  unexpected '}'
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * building 'cudasize_1.0.tar.gz'
>
>
> c:\Program Files\R\R-3.0.1\bin\i386>R CMD INSTALL --no-multiarch 
> cudasize_1.0.tar.gz
> R CMD INSTALL --no-multiarch cudasize_1.0.tar.gz
> * installing to library 'c:/myRlib'
> * installing *source* package 'cudasize' ...
> ** libs
> nvcc -m32 --shared -o cuda4.dll cuda4.cu
> cuda4.cu
> tmpxft_12fc_-5_cuda4.cudafe1.gpu
> tmpxft_12fc_-10_cuda4.cudafe2.gpu
> cuda4.cu
> tmpxft_12fc_-5_cuda4.cudafe1.cpp
> tmpxft_12fc_-15_cuda4.ii
> installing to c:/myRlib/cudasize/libs/i386
> ** R
> ** preparing package for lazy loading
> ** help
> Warning: 
> C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:33:
>  unexpected '{'
> Warning: 
> C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:37:
>  unexpected '}'
> Warning: 
> C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:31:
>  All text must be in a section
> Warning: 
> C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:32:
>  All text must be in a section
> Warning: 
> C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:34:
>  All text must be in a section
> Warning: 
> C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:35:
>  All text must be in a section
> Warning: 
> C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:36:
>  All text must be in a section
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> * DONE (cudasize)
>
> c:\Program Files\R\R-3.0.1\bin\i386>R --vanilla
> R --vanilla
>
> R version 3.0.1 (2013-05-16) -- "Good Sport"
> Copyright (C) 2013 The R Foundation for Statistical Computing
> Platform: i386-w64-mingw32/i386 (32-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information an

Re: [Rd] question about Makeconf and nvcc/CUDA

[Hodgess, Erin]

Wow!

This is just amazing!

Thanks so much.  I didn't realize how intense this is.



From: Duncan Temple Lang [dtemplel...@ucdavis.edu]
Sent: Thursday, July 18, 2013 3:08 PM
To: Hodgess, Erin
Cc: r-devel@r-project.org
Subject: Re: [Rd] question about Makeconf and nvcc/CUDA

Hi Erin

See the code below.

Basically, I have created a new routine that you will
call from R as

 .C("cuda4", 1L, "5")

where 1L is the number of arguments you are passing and "5" is the character 
vector of arguments.

We are using .C() here for simplicity. For other cases involving data, .Call() 
would be better.

That cuda4 routines is now not name-mangled, and has the correct parameter 
types and return type
to be called via the .C().
The good thing is this has nothing to do with CUDA, but just calling C++ 
routines from R.


This illustrates that there are complexities here with different devices, 
languages, etc.
This is one of the reasons a high-level interface to calling kernels is simpler 
and
more flexible.

The following R only code invokes the kernel on actual data we have in R (x).

# Put the square_array routine only in a file named, erinHodgess.cu
# add extern "C" before the square_array routine

  # generate the PTX code
f = nvcc("erinHodgess.cu")

  # load the PTX code
mod = loadModule(f)

  # Invoke the PTX code
x = rnorm(10)
ans = .gpu(mod$square_array, x, length(x), gridBy = x)

all.equal(x*x, ans)


  D.




#include 
#include 

// Kernel that executes on the CUDA device
extern "C"
__global__ void square_array(float *a, int N)
{
  int idx = blockIdx.x * blockDim.x + threadIdx.x;
  if (idx>> (a_d, N);
  // Retrieve result from device and store it in host array
  cudaMemcpy(a_h, a_d, sizeof(float)*N, cudaMemcpyDeviceToHost);
  // Print results
  for (int i=0; i Hi again.
>
> I put in the extern statement.
>
> However, I'm not sure what you mean by changing the signature, please.
>
> I changed out the routine name from "stuff" to "cuda4" in the cuda4.cu 
> program.
>
> Still getting:
>
>> library(cudasize)
> library(cudasize)
>
>>
>
>> .C("cuda4",as.character(5))
> .C("cuda4",as.character(5))
> Error in .C("cuda4", as.character(5)) :
>   C symbol name "cuda4" not in load table
> Execution halted
>
> c:\Program Files\R\R-3.0.1\bin\i386>
>
> I still want to keep at it.
>
> Thanks so much for all of your help!!!
>
> Erin
>
> 
> From: Duncan Temple Lang [dtemplel...@ucdavis.edu]
> Sent: Thursday, July 18, 2013 1:09 PM
> To: Hodgess, Erin
> Cc: r-devel@r-project.org
> Subject: Re: [Rd] question about Makeconf and nvcc/CUDA
>
> Hi Erin
>
> It appears that there is only one file in src that is compile, i.e. cuda4.cu.
>
> That does not contain a routine named cuda4, which is what you are trying to 
> invoke
> via the .Call("cuda4") expression.
>
> Instead, it contains two routines - one kernel square_array which runs
> on the GPU, and the routine stuff.
>
> To be able to call the stuff() routine from R, you would have to
> a)  add
>   extern "C"
> before its definition/declaration so that its name is not mangled by nvcc
>
> b)  change its signature so that it can be invoked via a .Call() or 
> alternatively
> a .C().
>
>  I would create another routine that acts as an intermediate routine
> called from R that then calls stuff().
>
> This assumes that what you showed us of cuda4.cu is all there is in it.
>D.
>
> On 7/18/13 11:01 AM, Hodgess, Erin wrote:
>> Hi again:
>>
>> Here is another problem that I am having.  Hope this will be the last one.  
>> I really want to see if I can put it together.  Sorry for belaboring the 
>> issue.
>>
>> Well, here is my story:
>>
>> c:\Program Files\R\R-3.0.1\bin\i386>R CMD build cudasize
>> R CMD build cudasize
>> * checking for file 'cudasize/DESCRIPTION' ... OK
>> * preparing 'cudasize':
>> * checking DESCRIPTION meta-information ... OK
>> * cleaning src
>> Warning: 
>> C:/Users/erin/AppData/Local/Temp/RtmpOKsfga/Rbuild22e066bf13fb/cudasize/man/f1.Rd:33:
>>  unexpected '{'
>> Warning: 
>> C:/Users/erin/AppData/Local/Temp/RtmpOKsfga/Rbuild22e066bf13fb/cudasize/man/f1.Rd:37:
>>  unexpected '}'
>> * checking for LF line-endings in source and make files
>> * checking for empty or unneeded directories
>> * building 'cudasize_1.0.tar.gz'
>>
>>
>> c:\Program Files\R\R-3.0.1\bin\i386>R CMD INSTALL --n

Re: [Rd] question about Makeconf and nvcc/CUDA

[Hodgess, Erin]

 index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
prepare_Rd: f1.Rd:33: unexpected '{'
prepare_Rd: f1.Rd:37: unexpected '}'
prepare_Rd: f1.Rd:31: All text must be in a section
prepare_Rd: f1.Rd:32: All text must be in a section
prepare_Rd: f1.Rd:34: All text must be in a section
prepare_Rd: f1.Rd:35: All text must be in a section
prepare_Rd: f1.Rd:36: All text must be in a section
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... ERROR
Running examples in 'cudasize-Ex.R' failed
The error most likely occurred in:

> ### Name: cudasize-package
> ### Title: test for cuda
> ### Aliases: cudasize-package cudasize
> ### Keywords: package
> 
> ### ** Examples
> 
> require(cudasize)
> z <- .Call("cuda4",1L,"5")
Error in .Call("cuda4", 1L, "5") : 
  C symbol name "cuda4" not in load table
Execution halted

c:\Program Files\R\R-3.0.1\bin\i386>

The updated cuda4.dll and symbols.rd files are in 
cudasize.Rcheck/00_pkg/cudasize/src

Yet again, any help truly appreciated.

Sincerely,
Erin




From: Duncan Temple Lang [dtemplel...@ucdavis.edu]
Sent: Thursday, July 18, 2013 3:08 PM
To: Hodgess, Erin
Cc: r-devel@r-project.org
Subject: Re: [Rd] question about Makeconf and nvcc/CUDA

Hi Erin

See the code below.

Basically, I have created a new routine that you will
call from R as

 .C("cuda4", 1L, "5")

where 1L is the number of arguments you are passing and "5" is the character 
vector of arguments.

We are using .C() here for simplicity. For other cases involving data, .Call() 
would be better.

That cuda4 routines is now not name-mangled, and has the correct parameter 
types and return type
to be called via the .C().
The good thing is this has nothing to do with CUDA, but just calling C++ 
routines from R.


This illustrates that there are complexities here with different devices, 
languages, etc.
This is one of the reasons a high-level interface to calling kernels is simpler 
and
more flexible.

The following R only code invokes the kernel on actual data we have in R (x).

# Put the square_array routine only in a file named, erinHodgess.cu
# add extern "C" before the square_array routine

  # generate the PTX code
f = nvcc("erinHodgess.cu")

  # load the PTX code
mod = loadModule(f)

  # Invoke the PTX code
x = rnorm(10)
ans = .gpu(mod$square_array, x, length(x), gridBy = x)

all.equal(x*x, ans)


  D.




#include 
#include 

// Kernel that executes on the CUDA device
extern "C"
__global__ void square_array(float *a, int N)
{
  int idx = blockIdx.x * blockDim.x + threadIdx.x;
  if (idx>> (a_d, N);
  // Retrieve result from device and store it in host array
  cudaMemcpy(a_h, a_d, sizeof(float)*N, cudaMemcpyDeviceToHost);
  // Print results
  for (int i=0; i Hi again.
>
> I put in the extern statement.
>
> However, I'm not sure what you mean by changing the signature, please.
>
> I changed out the routine name from "stuff" to "cuda4" in the cuda4.cu 
> program.
>
> Still getting:
>
>> library(cudasize)
> library(cudasize)
>
>>
>
>> .C("cuda4",as.character(5))
> .C("cuda4",as.character(5))
> Error in .C("cuda4", as.character(5)) :
>   C symbol name "cuda4" not in load table
> Execution halted
>
> c:\Program Files\R\R-3.0.1\bin\i386>
>
> I still want to keep at it.
>
> Thanks so much for all of your help!!!
>
> Erin
>
> 
> From: Duncan Templ