Re: [Rd] URW Fonts Description in Installation and Administration Manual

[Ramon Diaz-Uriarte]

On Wed, 30-12-2015, at 21:08, Dirk Eddelbuettel  wrote:
> On 30 December 2015 at 20:07, Ramon Diaz-Uriarte wrote:
> | 
> | 
> | 
> | On Wed, 30-12-2015, at 12:44, Dirk Eddelbuettel  wrote:
> | > On 30 December 2015 at 05:00, Dario Strbenac wrote:
> | > | Good day,
> | > | 
> | > | In section A.2, the manual advises "Linux users will want the urw-fonts 
> package". However, this package only seems to be available for RedHat Linux 
> and Fedora Linux. What about for Debian or Ubuntu ? There is no urw-fonts 
> package for them. Are there any other packages not mentioned that are 
> important for these two distributions ?
> | >
> | > edd@max:~$ apt-cache search urw | grep texlive
> | > texlive-fonts-recommended - TeX Live: Recommended fonts
> | > texlive-fonts-extra - TeX Live: Additional fonts
> | > edd@max:~$ 
> | 
> | Humm... on a Debian system (mix of unstable and testing) that shows
> | nothing.
>
> Really? I just fired up Docker instance with Debian 8.2 and saw it there, also
>
>   https://packages.debian.org/sid/texlive-fonts-recommended
>   https://packages.debian.org/sid/texlive-fonts-extra
>
> has it.  Otherwise, agreed that a search for URW reveals more

Yes, that is true. But I tried on another testing+unstable system and still

apt-cache search urw | grep texlive

gives me nothing.



> packages. Methinks this issue is specific to Dario's setup...

And mine might also be kind of strange :-). Oh well.



>
> Dirk


-- 
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Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
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Re: [Rd] URW Fonts Description in Installation and Administration Manual

[Ramon Diaz-Uriarte]

On Wed, 30-12-2015, at 12:44, Dirk Eddelbuettel  wrote:
> On 30 December 2015 at 05:00, Dario Strbenac wrote:
> | Good day,
> | 
> | In section A.2, the manual advises "Linux users will want the urw-fonts 
> package". However, this package only seems to be available for RedHat Linux 
> and Fedora Linux. What about for Debian or Ubuntu ? There is no urw-fonts 
> package for them. Are there any other packages not mentioned that are 
> important for these two distributions ?
>
> edd@max:~$ apt-cache search urw | grep texlive
> texlive-fonts-recommended - TeX Live: Recommended fonts
> texlive-fonts-extra - TeX Live: Additional fonts
> edd@max:~$ 

Humm... on a Debian system (mix of unstable and testing) that shows
nothing.  But


ramon@Bufo:~$ apt-cache search urw | grep tex
fonts-texgyre - OpenType fonts based on URW Fonts
tex-gyre - scalable PostScript and OpenType fonts based on URW Fonts
python-urwid-satext - collection of urwid widgets
ramon@Bufo:~$


shows two possibly relevant packages.


(Maybe this is a Ubuntu/Debian difference? I think Dirk has some machines
running Ubuntu).

Best,

R.


>
> Both packages list URW fonts promimently in their Description:
>
> Dirk


-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

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Re: [Rd] Writing my first CRAN vignette

[Ramon Diaz-Uriarte]

On Sun, 18-05-2014, at 19:19, Dirk Eddelbuettel  wrote:
> On 18 May 2014 at 11:34, Hadley Wickham wrote:
> | > I am intending to use Sweave. I have read the Sweave documentation and
> | > section 1.4 of the extensions manual and apart from (a) do not use split =
> | > TRUE (b) and include all the source components, there does not seem to be
> | > anything CRAN specific.
> | 
> | I'd strongly recommend using knitr instead - the biggest advantage is
> | that you can use markdown, which is substantially easier to use than
> | latex (and doesn't require such a massive toolchain)
>
> Markdown is very useful. And it keeps getting better -- shiny-within-markdow
> is / will rock very, very hard.
>
> But there are also some things that I still much prefer to be in pdf form,
> rather than (in however well-styled) html and browser content.  And some
> paths in the toolchain that leads content from markdown to pdf are via latex,
> so you end up using latex anyway. Which isn't really that hard to install on
> any of the three main platforms as texlive bundles it pretty well.
>
> And more generally, a vignette is (at least to me, but also some others)

To me too. But still, with knitr he can use as much latex as with Sweave.


> still a 'paper' -- something that strives to be something like an academic
> article (and occassionally even manages to get there).  
>
> And for that form of written communication, I fear you will have to pry latex
> from my cold dead hands.

:-). 


R.


>
> Dirk


-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina 
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

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Re: [Rd] .Call ref card

[Ramon Diaz-Uriarte]

Peter, thanks for the slides. However, I felt like Terry and I think
because I am missing the "big picture" that I was somewhat surprised by
some of the content and organization (e.g., the detail about character
vectors, the usage of the tcltk package as example code).

Best,

R.


On Thu, 22 Mar 2012 12:45:14 -0500,Terry Therneau  wrote:
> On 03/22/2012 11:03 AM, peter dalgaard wrote:
> > Don't know how useful it is any more, but back in the days, I gave this 
> > talk in Vienna
> >
> > http://www.ci.tuwien.ac.at/Conferences/useR-2004/Keynotes/Dalgaard.pdf
> >
> > Looking at it now, perhaps it moves a little too quickly into the hairy 
> > stuff. On the other hand, those were the things that I had found important 
> > to figure out at the time. At a quick glance, I didn't spot anything 
> > obviously outdated.
> >
> Peter,
>I just looked at this, and I'd say that moved into the hairy stuff 
> way too quickly.  Much of what it covered I would never expect to use.  
> Some I ddn't understand.  Part of this of course is that slides for a 
> talk are rarely very useful without the talker.

>   Something simpler for the layman would be good.

> Terry T.

-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina 
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

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[Rd] .Call ref card [was Re: R-devel Digest, Vol 109, Issue 22]

[Ramon Diaz-Uriarte]

> > and we should keep that in mind before getting too pompous in our lectures 
> > to the "sinners of .C".  (Mostly because the things I needed to know are 
> > scattered about in multiple places.)
> > 
> > I might have to ask for an exemption on that timestamp -- the first bits of 
> > the survival package only reach back to 1986.  And I've had to change 
> > source code systems multiple times which plays hob with the file times, 
> > though I did try to preserve the changelog history to forstall some future 
> > litigious soul who claims they wrote it first  (sccs -> rcs -> cvs -> svn 
> > -> mercurial).   :-)
> > 

> ;) Maybe the rule should be based on the date of the first appearance of the 
> package, fair enough :)

> Cheers,
> Simon
>   [[alternative HTML version deleted]]

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-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina 
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

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Re: [Rd] using zlib in a package: problems in windows

[Ramon Diaz-Uriarte]

Dear Prof. Ripley,

Thanks.

Best,

R.

On Tue, May 20, 2008 at 7:44 AM, Prof Brian Ripley
<[EMAIL PROTECTED]> wrote:
> gzprintf is not in Rzlib.dll.  It has been commented out in the R build.
> So you will need to use you own copy of zlib.
>
> On Tue, 20 May 2008, Ramon Diaz-Uriarte wrote:
>
>> Dear All,
>>
>> I am having trouble getting an R package to build and install
>> correctly under Windows. In this package, which builds and checks OK
>> under Linux, I use zlib (among other functions, gzprintf).
>>
>> As mentioned by Prof. Ripley a while back, the file "CHANGES" under
>> src/gnuwin32 says explains that to, to use zlib, one has to set
>> $(ZLIB_LIBS) in PKG_LIBS. I have a Makefile.win with just that.
>>
>> I have also downloaded the Windows toolset (Rtools.exe) which I have
>> used to successfully build R-patched. However, I still cannot get the
>> package to compile.
>>
>>> From the log, it seems that in fact the build is trying to use zlib,
>>
>> but the gzprintf symbol is not found. However, gzprintf is in the
>> zlib.h header.  00install.out follows below.
>>
>> What am I doing wrong?
>>
>> Thanks,
>>
>> R.
>>
>> P.D. I am using Windows 2000 (under vmware).
>>
>>
>>
>>
>> -- Making package RJaCGH 
>>
>>  **
>>  WARNING: this package has a configure script
>>It probably needs manual configuration
>>  **
>>
>>  adding build stamp to DESCRIPTION
>>  installing NAMESPACE file and metadata
>>  making DLL ...
>> making nnhl.d from nnhl.c
>> gcc  -std=gnu99  -Ic:/R/R-patc~1/include -O3 -Wall  -c nnhl.c -o
>> nnhl.o
>> windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I
>> c:/R/R-patc~1/include  -i RJaCGH_res.rc -o RJaCGH_res.o
>> gcc  -std=gnu99  -shared -s  -o RJaCGH.dll RJaCGH.def nnhl.o
>> RJaCGH_res.o  -Lc:/R/R-patc~1/bin -lRzlib   -lR
>> nnhl.o:nnhl.c:(.text+0x138f): undefined reference to `gzprintf'
>> nnhl.o:nnhl.c:(.text+0x13ae): undefined reference to `gzprintf'
>> nnhl.o:nnhl.c:(.text+0x13d2): undefined reference to `gzprintf'
>> nnhl.o:nnhl.c:(.text+0x13f6): undefined reference to `gzprintf'
>> nnhl.o:nnhl.c:(.text+0x1415): undefined reference to `gzprintf'
>> nnhl.o:nnhl.c:(.text+0x1451): more undefined references to `gzprintf'
>> follow
>> collect2: ld returned 1 exit status
>> make[3]: *** [RJaCGH.dll] Error 1
>> make[2]: *** [srcDynlib] Error 2
>> make[1]: *** [all] Error 2
>> make: *** [pkg-RJaCGH] Error 2
>> *** Installation of RJaCGH failed ***
>>
>>
>>
>>
>> --
>> Ramon Diaz-Uriarte
>> Statistical Computing Team
>> Structural Biology and Biocomputing Programme
>> Spanish National Cancer Centre (CNIO)
>> http://ligarto.org/rdiaz
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
> --
> Brian D. Ripley,  [EMAIL PROTECTED]
> 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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Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz

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[Rd] using zlib in a package: problems in windows

[Ramon Diaz-Uriarte]

Dear All,

I am having trouble getting an R package to build and install
correctly under Windows. In this package, which builds and checks OK
under Linux, I use zlib (among other functions, gzprintf).

As mentioned by Prof. Ripley a while back, the file "CHANGES" under
src/gnuwin32 says explains that to, to use zlib, one has to set
$(ZLIB_LIBS) in PKG_LIBS. I have a Makefile.win with just that.

I have also downloaded the Windows toolset (Rtools.exe) which I have
used to successfully build R-patched. However, I still cannot get the
package to compile.

>From the log, it seems that in fact the build is trying to use zlib,
but the gzprintf symbol is not found. However, gzprintf is in the
zlib.h header.  00install.out follows below.

What am I doing wrong?

Thanks,

R.

P.D. I am using Windows 2000 (under vmware).




-- Making package RJaCGH 

   **
   WARNING: this package has a configure script
 It probably needs manual configuration
   **

  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making nnhl.d from nnhl.c
gcc  -std=gnu99  -Ic:/R/R-patc~1/include -O3 -Wall  -c nnhl.c -o nnhl.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I
c:/R/R-patc~1/include  -i RJaCGH_res.rc -o RJaCGH_res.o
gcc  -std=gnu99  -shared -s  -o RJaCGH.dll RJaCGH.def nnhl.o
RJaCGH_res.o  -Lc:/R/R-patc~1/bin -lRzlib   -lR
nnhl.o:nnhl.c:(.text+0x138f): undefined reference to `gzprintf'
nnhl.o:nnhl.c:(.text+0x13ae): undefined reference to `gzprintf'
nnhl.o:nnhl.c:(.text+0x13d2): undefined reference to `gzprintf'
nnhl.o:nnhl.c:(.text+0x13f6): undefined reference to `gzprintf'
nnhl.o:nnhl.c:(.text+0x1415): undefined reference to `gzprintf'
nnhl.o:nnhl.c:(.text+0x1451): more undefined references to `gzprintf' follow
collect2: ld returned 1 exit status
make[3]: *** [RJaCGH.dll] Error 1
make[2]: *** [srcDynlib] Error 2
make[1]: *** [all] Error 2
make: *** [pkg-RJaCGH] Error 2
*** Installation of RJaCGH failed ***




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Spanish National Cancer Centre (CNIO)
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Re: [Rd] returning vectors of unknown size from C (with .C)

[Ramon Diaz-Uriarte]

On Sat, Apr 26, 2008 at 11:38 AM, Prof Brian Ripley
<[EMAIL PROTECTED]> wrote:
> On Sat, 26 Apr 2008, Ramon Diaz-Uriarte wrote:
>
>
> > On Sat, Apr 26, 2008 at 3:19 AM, Duncan Murdoch <[EMAIL PROTECTED]>
> wrote:
> >
> > > Ramon Diaz-Uriarte wrote:
> > >
> > >
> > > > Dear All,
> > > >
> > > > In a package, I am using ".C" to call some C functions. In one case,
> > > > the number of elements of the return vectors are not known in R before
> > > > the C call. (Two of the vectors are integers, the third is vector of
> > > > character strings).
> > > >
> > > > Passing from R a vector of the maximum possible size would be a huge
> > > > waste. I understand one alternative is to use ".Call", but I'd rather
> > > > avoid it if I can (all of the code seems working except for the return
> > > > of values into R). Another would be to write to a file from C and then
> > > > read that into R, but this looks very ugly. Are there any other
> > > > reasonable alternatives, or should I just use .Call?
> > > >
> > > >
> > > >
> > >
> > >  .Call is usually easiest, but another possibility is to have two entry
> > > points:  one to calculate how much space you need, a second to pass in a
> > > vector that's the right size to hold the result.
> > >
> > >
> >
> >
> > You mean making two successive calls to the C code? The problem is
> > that the size of the result is not known until the result is obtained
> > (in my C code, the underlying structure is a linked list that gets
> > stretched as needed as the computation proceeds). So I would not know
> > "where to leave the result from C" in between the two calls to C.
> >
>
>  But that is possible (you malloc the memory for a local copy in the rist
> call), and rpart does something like it.
>

Aha, thanks, I didn't know it was doable (or easy). I'll look at the
rpart code. One further question, though, what is "the rist call"?

Thanks,

R.


>
>  --
>  Brian D. Ripley,  [EMAIL PROTECTED]
>  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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Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz

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Re: [Rd] returning vectors of unknown size from C (with .C)

[Ramon Diaz-Uriarte]

On Sat, Apr 26, 2008 at 3:19 AM, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
> Ramon Diaz-Uriarte wrote:
>
> > Dear All,
> >
> > In a package, I am using ".C" to call some C functions. In one case,
> > the number of elements of the return vectors are not known in R before
> > the C call. (Two of the vectors are integers, the third is vector of
> > character strings).
> >
> > Passing from R a vector of the maximum possible size would be a huge
> > waste. I understand one alternative is to use ".Call", but I'd rather
> > avoid it if I can (all of the code seems working except for the return
> > of values into R). Another would be to write to a file from C and then
> > read that into R, but this looks very ugly. Are there any other
> > reasonable alternatives, or should I just use .Call?
> >
> >
>
>  .Call is usually easiest, but another possibility is to have two entry
> points:  one to calculate how much space you need, a second to pass in a
> vector that's the right size to hold the result.
>


You mean making two successive calls to the C code? The problem is
that the size of the result is not known until the result is obtained
(in my C code, the underlying structure is a linked list that gets
stretched as needed as the computation proceeds). So I would not know
"where to leave the result from C" in between the two calls to C.

Best,

R.




>  Duncan Murdoch
>
> > Thanks,
> >
> > R.
> >
> >
> >
> >
> >
>
>



-- 
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Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
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[Rd] returning vectors of unknown size from C (with .C)

[Ramon Diaz-Uriarte]

Dear All,

In a package, I am using ".C" to call some C functions. In one case,
the number of elements of the return vectors are not known in R before
the C call. (Two of the vectors are integers, the third is vector of
character strings).

Passing from R a vector of the maximum possible size would be a huge
waste. I understand one alternative is to use ".Call", but I'd rather
avoid it if I can (all of the code seems working except for the return
of values into R). Another would be to write to a file from C and then
read that into R, but this looks very ugly. Are there any other
reasonable alternatives, or should I just use .Call?

Thanks,

R.



-- 
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Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz

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Re: [Rd] Rmpi and OpenMPI ?

[Ramon Diaz-Uriarte]

On Friday 30 March 2007 22:01, Dirk Eddelbuettel wrote:
> On 30 March 2007 at 12:48, Ei-ji Nakama wrote:
> | Prof. Nakano(ism Japan) and I wrestled in Rmpi on HP-MPI.
> | Do not know a method to distinguish MPI well?
> | It is an ad-hoc patch at that time as follows.
>
> Thank you *very much* for this.  I tried an ad-hoc patch that did about
> half of this (i.e. coping with configure, and not letting zzz.R play with
> lamboot) which let to Rmpi at least building ... but not yet running.
>
> I will look more closely at what needs to happen at the C/C++ level in MPI
> and see if I can (eventually) put the rest together.
>
> As for your question about distinguishing MPI implementations: Not sure
> yet. Under Debian, I had to un-install the lam and mpich2 development
> packages as configure would otherwise find their mpi.h first.  I'll have to
> see if there is a canonical / portable identifier for MPI.
>
> For anybody else reading along, this appears to be a great resource (and it
> requires a free registration for webct):
>
>   http://webct.ncsa.uiuc.edu:8900/public/MPI/


Thanks for the link! Looks really nice indeed.

Best,

R.

>
> Regards,  Dirk

-- 
Ramón Díaz-Uriarte
Statistical Computing Team
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

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Re: [Rd] Rmpi and OpenMPI ?

[Ramon Diaz-Uriarte]

Hi Dirk,

On Wednesday 28 March 2007 04:34, Dirk Eddelbuettel wrote:
> Has anybody tried to use Rmpi with the OpenMPI library instead of LAM/MPI?
>

I have not, but I'd be very interested in whatever you find. One thing that 
stopped me as soon as I considered it is that, if I understand correctly, 
there is (still) nothing in OpenMPI like the "lamboot" command of LAM/MPI 
(and that is a crucial part of our set up).

Best,

R.



> LAM appears to be somewhat hardcoded in the Rmpi setup. Before I start to
> experiment with changing this, has anybody else tried Rmpi with non-LAM MPI
> implementations?
>
> Dirk






-- 
Ramón Díaz-Uriarte
Statistical Computing Team
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
(http://ligarto.org/rdiaz/0xE89B3462.asc)



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Re: [Rd] IDE for R C++ package writing ?

[Ramon Diaz-Uriarte]

On Monday 26 February 2007 16:51, [EMAIL PROTECTED] wrote:
> > First, great thanks to all for all the answers. I confess i was a bit
> > scared about (re)learning a possible tomorrow obsolete tool.
> >
> > I'm however quite astonished nobody proposes another tool. Do 100% R
> > package developers use emacs ?
>
> Plenty of folks don't use an IDE at all.  Copy/pasting working bits of
> code from your .Rhistory into a working file is a very useful tactic...

You kidding, right? (I mean, maybe lots of people do that, but maybe that 
ain't such a good idea :-).

R.

P.S. Whether or not emacs + ess + ecb + a whole bunch of other things is or 
not a "real IDE" (whatever that means) I think is tangential to the original 
question. The issue, if I understand, are editing tools that will make the 
editing et al. simpler. So 

> > I'm however quite astonished nobody proposes another tool. Do 100% R
> > package developers use emacs ?
>

No. Not 100%. But you said you'll be using Windows but want to move to 
GNU/Linux. Then, you might want to use the very same tool over a range of 
OSs, or regardless of whether you are in front of your workstation, or 
accessing it over a slow modem connection, etc. In such cases, Emacs is an 
excellent choice. Or one of the very, very few. In addition, I think you are 
seeing an example of  "once you try emacs, you often realize that other 
choices do not really offer you all that much, but you loose a lot". 

HTH,

R.


>
> --e
>
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Re: [Rd] IDE for R C++ package writing ?

[Ramon Diaz-Uriarte]

On Friday 23 February 2007 15:52, Marc Schwartz wrote:
> In addition to Prof. Ripley's comments, which I wholeheartedly support,
> I might point you to some additional tools, that enhance the use of
> Emacs for coding.
>
> I am running Emacs (alpha version 23 from cvs source) under Linux and
> while I do not do C, C++ or FORTRAN coding, these tools have
> dramatically improved my coding productivity when using R and Sweave (R
> + LaTeX) along with ESS and other standard Emacs tools such as
> Auctex/Preview-Latex.
>
>
> 1. ECB - Emacs Code Browser
>
>   http://ecb.sourceforge.net/
>
>
> 2. psvn - A Subversion interface for emacs
>
>   http://www.xsteve.at/prg/vc_svn/
>
>
> Both of the above, especially if you integrate version control using
> Subversion, greatly enhance the functionality of Emacs as an IDE.
>
> HTH,
>
> Marc Schwartz


Just a minor addition to Marc's comment: if you edit Python code, you might 
experience short, but frequent, freezes of Emacs that are related to a 
problem with semantic (a package on which ECB depends). I've not seen these 
with R (or C/C++ or LaTeX).

With that minor caveat, I find ECB is a great tool that works out of the box 
with R.

Best,

R.


>
> On Fri, 2007-02-23 at 11:17 +, Prof Brian Ripley wrote:
> > You seem to mention both Linux and Windows.
> >
> > Emacs and XEmacs are both stable on both platforms, and I think most R
> > developers use an emacs or vi variant for all their programming.  I would
> > not call emacs an IDE, but the main thing I find useful is to have a
> > language-aware editor (syntax highlighting, indentation ...).
> >
> > If you write a package you will also need an Rd editor, and emacs/ESS is
> > probably the best supported of those.
> >
> > Later versions of precompiled emacs for Windows have existed, but I am
> > running 21.3.1 (2002) on Windows and 21.4.1 on Linux: emacs itself is
> > very stable.  If you prefer a more graphical environment, XEmacs is a
> > good alternative and despite its name has an active Windows version.
> >
> > On Fri, 23 Feb 2007, mel wrote:
> > > Dear all,
> > >
> > > I have to develop a (hopefully) small package for R in C++.
> > > I didn't code in C++ for some years, and i'm now searching
> > > for an adequate IDE for this task.
> > >
> > > Some of my criterions : not proprietary, not too heavy,
> > > open to linux, not java gasworks, still maintained, etc
> > >
> > > After looking on several places
> > > http://en.wikipedia.org/wiki/List_of_C%2B%2B_compilers_and_integrated_d
> > >evelopment_environments
> > > http://www.freeprogrammingresources.com/cppide.html
> > > + R docs
> > > I was thinking on code::blocks, and emacs (and perhaps vim)
> > >
> > > Emacs seems used by some R developers as an R editor.
> > > So i did think on emacs because it could perhaps be interesting
> > > to have the same editor for R code and C++ code.
> > >
> > > However, when looking at the last emacs windows version,
> > > it seems to date from january 2004 ... (dead end ?)
> > > ftp://ftp.gnu.org/pub/gnu/emacs/windows/
> > >
> > > I will be grateful for all advices on this tool topic.
> > > Better choosing emacs ? or code::blocks ?
> > > or another idea ?
> > > Does somebody have an idea about the most used IDEs for
> > > R C++ package writing ?
> > >
> > > Thanks
> > > Vincent
>
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28029 Madrid (Spain)
Fax: +-34-91-224-6972
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Re: [Rd] IDE for R C++ package writing ?

[Ramon Diaz-Uriarte]

On Friday 23 February 2007 11:49, mel wrote:
> Dear all,
>
> I have to develop a (hopefully) small package for R in C++.
> I didn't code in C++ for some years, and i'm now searching
> for an adequate IDE for this task.
>
> Some of my criterions : not proprietary, not too heavy,
> open to linux, not java gasworks, still maintained, etc
>
> After looking on several places
> http://en.wikipedia.org/wiki/List_of_C%2B%2B_compilers_and_integrated_devel
>opment_environments http://www.freeprogrammingresources.com/cppide.html
> + R docs
> I was thinking on code::blocks, and emacs (and perhaps vim)
>
> Emacs seems used by some R developers as an R editor.
> So i did think on emacs because it could perhaps be interesting
> to have the same editor for R code and C++ code.
>
> However, when looking at the last emacs windows version,
> it seems to date from january 2004 ... (dead end ?)
> ftp://ftp.gnu.org/pub/gnu/emacs/windows/
>
> I will be grateful for all advices on this tool topic.
> Better choosing emacs ? or code::blocks ?
> or another idea ?
> Does somebody have an idea about the most used IDEs for
> R C++ package writing ?


Dear Vincent,

I wouldn't let the date of 2004 scare you away from emacs. And, if I 
understand, in windows you can also use xemacs and/or emacs. 

One extremely nice feature of using Emacs is using the very same editor for R, 
C, C++, or anything else for that matter. It certainly fits your other 
requirements

> Some of my criterions : not proprietary, not too heavy,
> open to linux, not java gasworks, still maintained, etc

Good luck!

R.



>
> Thanks
> Vincent
>
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Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

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Re: [Rd] Speed of for loops

[Ramon Diaz-Uriarte]

On Tuesday 30 January 2007 15:46, Tamas K Papp wrote:
> On Tue, Jan 30, 2007 at 12:15:29PM +, Oleg Sklyar wrote:
> > magnitude using c-functions for "complex" vector indexing operations. If
> > you need instructions, I can send you a very nice "Step-by-step guide
> > for using C/C++ in R" which goes beyond "Writing R Extensions" document.
>
> Hi Oleg,
>
> Can you please post this guide online?  I think that many people would
> be interested in reading it, incl. me.
>

Me too.

Thanks,

R.

> Tamas
>
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Re: [Rd] C vs. C++ as learning and development tool for R

[Ramon Diaz-Uriarte]

Dear Mark,

On Friday 19 January 2007 09:55, Kimpel, Mark William wrote:
> I have 3 years of experience with R and have an interest in becoming a
> better programmer so that I might someday be able to contribute
> packages. Other than R, my only experience was taking Lisp from Daniel
> Friedman in the 1970's. I would like to learn either C or C++ for
> several reasons:
>
> To gain a better concept of object oriented programming so that I can
> begin to use S4 methods in R.
>

I do not think C++ is the best idea if you are learning it to understand the 
OOP of R. The OOP of R is probably closer to that of CLOS (the common lisp 
object system) than C++ and Java.

It might be better to directly go ahead and look for documentation specificaly 
about R's OOP.

> To perhaps speed up some things I do repeatedly in R
>
> To be able to contribute a package someday.
>
>
>
> I have been doing some reading and from what I can tell R is more
> compatible with C, but C++ has much greater capabilities for OO
> programming.
>
>
>
> I have just started reading The C++ Programming Language: Special
> Edition by Bjarne Stroustrup
>  ustrup&z=y> , he recommends first learning C++ and then then C if
> necessary, but as a developer of C++, he is probably biased.
>
>
>
> I would greatly appreciate the advice of the R developers and package
> contributors on this subject. "C" or "C++"?
>
>

I'd recommend C instead of C++: C++ is a huge language and it is somewhat 
easier to interface C than C++ from R. (In "non-R" stuff I prefer to use C++ 
better than C, even if just as in "C++as a better C", but this probably is 
not a reasonable reason to learn C++).  

HTH,

R.



>
> Thanks,
>
>
>
> Mark
>
>
>
> Mark W. Kimpel MD
>
>
>
>
>
> Official Business Address:
>
>
>
> Department of Psychiatry
>
> Indiana University School of Medicine
>
> PR M116
>
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>
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>
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>
>
>
> Preferred Mailing Address:
>
>
>
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>
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>
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Re: [Rd] Cross-compilation

[Ramon Diaz-Uriarte]

Dear Tom,

It has worked for me out-of-the box in at least two times, one a while ago 
with R-2.2-something and recently with R-2.4.0. In both cases, I was running 
Debian (with a mix of testing and unstable) on x86. I never had to do 
anything, just run the script and at least in one case I did crosscompile a 
package with C++.


R.

On Wednesday 25 October 2006 18:03, Tom McCallum wrote:
> Hi everyone,
>
> I am trying to cross-compile a package I wrote using the Yan and Rossini
> tutorial "Building Microsoft Windows versions of R and R packages using
> Intel Linux".  I have got reasonably far with this but when doing the
> linking using the line:
>
> i586-mingw32-g++  -shared -s  -o mylibrary.dll mylibrary.def mylibrary.o
> mylibrary_res.o  -L/my/path/RCrossBuild/WinR/R-2.4.0/bin -lR
>
> I get lots of these type of messages:
> /my/path/to/mylibrary.cpp:43: undefined reference to
> `_GLOBAL_OFFSET_TABLE_'
>
> and other similar linker errors for virtually every object and command in
> the program.  After some googling I have found that there may be problems
> with the libgcc.a library and its default -fPIC argument during
> compilation.
>
> Has anyone got this tutorial to work and if so how did they overcome this?
>
> I am attempting to do this on Fedora Core 4 on a 32-bit machine, having
> completed all the previous sections of the tutorial for building a
> cross-platform version of R.
>
> Many thanks
>
> Tom

-- 
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Bioinformatics 
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(Spanish National Cancer Center)
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