Re: [Rd] http://cran.r-project.org/src/base/NEWS.html points to R v2.13.0

2011-08-30 Thread Uwe Ligges



On 29.08.2011 21:22, Henrik Bengtsson wrote:

FYI,

http://cran.r-project.org/src/base/NEWS.html [May 18, 2011] is for R
v2.13.0 whereas http://cran.r-project.org/src/base/NEWS [July 8, 2011]
is for R v2.13.1.  The former is linked to on a few places on
http://cran.r-project.org/.


Thnaks, probably the automatism that generates the NEWS does not yet 
generate the NEWS.html for CRAN. CCing CRAN@.. so this won't get 
lost in the mailing list archives.


Uwe





/Henrik

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Re: [Rd] http://cran.r-project.org/src/base/NEWS.html points to R v2.13.0

2011-08-30 Thread peter dalgaard

On Aug 30, 2011, at 11:21 , Uwe Ligges wrote:

 
 
 On 29.08.2011 21:22, Henrik Bengtsson wrote:
 FYI,
 
 http://cran.r-project.org/src/base/NEWS.html [May 18, 2011] is for R
 v2.13.0 whereas http://cran.r-project.org/src/base/NEWS [July 8, 2011]
 is for R v2.13.1.  The former is linked to on a few places on
 http://cran.r-project.org/.
 
 Thnaks, probably the automatism that generates the NEWS does not yet generate 
 the NEWS.html for CRAN. CCing CRAN@.. so this won't get lost in the 
 mailing list archives.
 


This was already noted by Kurt back in May and I promised to fix the 
R-build-dist script when I had a clear head after grading exams, which 
apparently never happened...

Done now (incl. CRAN). 


 Uwe
 
 
 
 
 /Henrik
 
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[Rd] Problem exporting table with many columns to dbf

2011-08-30 Thread Nacho Uve
Hello,

I'm newbie in R and I have a problem exporting a table with many columns to
a dbf file.
I found an error when I open the result DBF file on other software and also
importing it on R again.

Here a example snippet of the problem (on a GNU/Linux OS):
http://pastebin.com/0SMJqqwb

Is it a bug?

Thank you,
Nacho V

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[Rd] unexpected behavior of callNextMethod() when passing arguments in methods to generic function

2011-08-30 Thread hen...@singmann.org

Hi,
 
there seems to be an unexpected behavior when using callNextMethod() in a method
to a (user defined) generic function so that additional arguments to the ones
defined in the signature of the generic are not passed correctly (i.e., their
value are lost/replaced by the default).
 
Problem description:
We have two hierarchical classes, foo and subclass bar and a generic
function foobar. There exists methods for foobar for both foo and bar that
have the same signature, which differs from the signature in the generic
function (i.e., there are additional arguments in the methods).There are default
values for the additional arguments in the two methods.The method for bar
contains a callNextMethod() statement.
Now calling foobar for an object of class bar with an additional argument
set to a non-defualt value leads to: in the method for bar, the the additional
argument is equal to the input; in the method for foo (i.e., within the
callNextMethod() statement) the additional argument is equal to the default for
that method (i.e., instead of equal to the user input).
 
This behavior contrasts with my reading of ?callNextMethod which states:
For a formal argument, sayx, that appears in the original call, there is a
corresponding argument in the next method call equivalent tox = x. In effect,
this means that the next method sees the same actual arguments, but arguments
are evaluated only once.
 
Therefore I would expect the additional argument be passed on by
callNextMethod() as inputted by the user. 
 
Example:  

setClass(foo, representation(x = numeric))
setClass(bar, contains = foo)

setGeneric(foobar, function(object, ...) standardGeneric(foobar))

setMethod(foobar, foo, function(object, another.argument = FALSE, ...) {
    print(paste(another.argument in foo-method:, another.argument))
    object@x
})

setMethod(foobar, bar, function(object, another.argument = FALSE, ...) {
    print(paste(another.argument in bar-method:, another.argument))
    callNextMethod()
})

o1 - new(bar, x = 4)

 foobar(o1, another.argument = TRUE)
[1] another.argument in bar-method: TRUE
[1] another.argument in foo-method: FALSE
[1] 4
 

Related Issues:
I already asked this question on stackoverflow
(http://stackoverflow.com/q/7190697/289572) and got a helpful answer with
workarounds from Martin Morgan. However, I have the feeling that this may be of
interest here, too. 
This problem may or may not be related to the following similar bug reported on
r-devel: 
http://thread.gmane.org/gmane.comp.lang.r.devel/23263/focus=23266
 
Best,
Henrik 
 
 
PS:
 sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C    LC_TIME=English_United
Kingdom.1252   

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] fortunes_1.4-2

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Re: [Rd] How to safely using OpenMP pragma inside a .C() function?

2011-08-30 Thread Alireza Mahani
I have no R API calls inside the parallelized block. I will work on creating
a self-contained example and post it for your review. Thanks! -Alireza

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Re: [Rd] sysdata.rda, namespaces and package dependencies

2011-08-30 Thread Hadley Wickham
Bump.  Any comments on this?
Hadley

On Tue, Aug 16, 2011 at 10:53 AM, Hadley Wickham had...@rice.edu wrote:
 Hi all,

 I'm struggling with accessing a package dataset (munsell.map, stored
 in sysdata.rda) when that package is imported, not required.  A simple
 reproducible example is:

 install.packages(munsell)
 munsell::mnsl(10B 4/6)
 # Error in match(col, munsell.map$name) : object 'munsell.map' not found

 library(munsell)
 munsell::mnsl(10B 4/6)
 # Function works correctly

 Am I doing something wrong, or is this namespace bug?

 Hadley

 --
 Assistant Professor / Dobelman Family Junior Chair
 Department of Statistics / Rice University
 http://had.co.nz/




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Re: [Rd] sysdata.rda, namespaces and package dependencies

2011-08-30 Thread Yihui Xie
I struggled with this for a while too, and I have no idea why this
data object is unavailable. Finally I found this can do the trick:

data(munsell_map, package = munsell)
munsell::mnsl(10B 4/6)
## works

But I still cannot understand this.

Regards,
Yihui
--
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Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA



On Tue, Aug 30, 2011 at 8:27 AM, Hadley Wickham had...@rice.edu wrote:
 Bump.  Any comments on this?
 Hadley

 On Tue, Aug 16, 2011 at 10:53 AM, Hadley Wickham had...@rice.edu wrote:
 Hi all,

 I'm struggling with accessing a package dataset (munsell.map, stored
 in sysdata.rda) when that package is imported, not required.  A simple
 reproducible example is:

 install.packages(munsell)
 munsell::mnsl(10B 4/6)
 # Error in match(col, munsell.map$name) : object 'munsell.map' not found

 library(munsell)
 munsell::mnsl(10B 4/6)
 # Function works correctly

 Am I doing something wrong, or is this namespace bug?

 Hadley

 --
 Assistant Professor / Dobelman Family Junior Chair
 Department of Statistics / Rice University
 http://had.co.nz/




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 http://had.co.nz/

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Re: [Rd] sysdata.rda, namespaces and package dependencies

2011-08-30 Thread Hadley Wickham
 Your package is doing something weird, so I think it's you:  you are loading
 the munsell.map file via load.r in the top level of the package.  That's
 not a standard thing to do, and it's not being executed in the first case.

 Put that load statement into one of the files in the R directory and things
 should be fine.

I think that's a red-herring - load.r is for development and is never
run during usual package installation.  Or are you saying I need to
explicit load data stored in sysdata.rda within the package?

Hadley

-- 
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Department of Statistics / Rice University
http://had.co.nz/

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[Rd] Problems with r-help

2011-08-30 Thread Gabor Grothendieck
I am getting messages like this whenever I try to post to r-help.  The
message seems to say that the problem is with on the r-help end (the
recipient domain).


Delivery to the following recipient failed permanently:

r-h...@r-project.org

Technical details of permanent failure:
Google tried to deliver your message, but it was rejected by the
recipient domain. We recommend contacting the other email provider for
further information about the cause of this error. The error that the
other server returned was: 550 550-Callout verification failed:
550 550 5.7.1 Mail from 129.132.202.242 refused - see
http://www.orbitrbl.com/ (state 14).

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Re: [Rd] Problems with r-help

2011-08-30 Thread Gabor Grothendieck
On Tue, Aug 30, 2011 at 11:42 AM, Gabor Grothendieck
ggrothendi...@gmail.com wrote:
 I am getting messages like this whenever I try to post to r-help.  The
 message seems to say that the problem is with on the r-help end (the
 recipient domain).


 Delivery to the following recipient failed permanently:

    r-h...@r-project.org

 Technical details of permanent failure:
 Google tried to deliver your message, but it was rejected by the
 recipient domain. We recommend contacting the other email provider for
 further information about the cause of this error. The error that the
 other server returned was: 550 550-Callout verification failed:
 550 550 5.7.1 Mail from 129.132.202.242 refused - see
 http://www.orbitrbl.com/ (state 14).

It seems this was temporary since I was just able to post a test
message and an actual message to r-help.


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Re: [Rd] How to safely using OpenMP pragma inside a .C() function?

2011-08-30 Thread pawelm
Simon,

I found that files R-2.13.1/src/library/stats/src/distance.c and
R-2.13.1/src/main/array.c have openmp code (example below). I have couple
questions regarding best practices when using R internals and openmp. 

Can we use R-2.13.1/src/library/stats/src/distance.c and
R-2.13.1/src/main/array.c as an example how to interact with R code and R
internals?
What are my other options if I want to work with SEXP structures in my
parallel code?

Thank you
Regards

=

#ifdef HAVE_OPENMP
/* This gives a spurious -Wunused-but-set-variable error */
if (R_num_math_threads  0) 
nthreads = R_num_math_threads;
else 
nthreads = 1; /* for now */
#pragma omp parallel for num_threads(nthreads) default(none) \
private(j, i, ix, rx) \
firstprivate(x, ans, n, p, type, cnt, sum, \
 NaRm, keepNA, R_NaReal, R_NaInt, OP)
#endif
for (j = 0; j  p; j++) {
switch (type) {
case REALSXP:
rx = REAL(x) + n*j; 
if (keepNA)
for (sum = 0., i = 0; i  n; i++) sum += *rx++;
else {
for (cnt = 0, sum = 0., i = 0; i  n; i++, rx++)
if (!ISNAN(*rx)) {cnt++; sum += *rx;}
else if (keepNA) {sum = NA_REAL; break;}
}
break;
case INTSXP:
ix = INTEGER(x) + n*j; 
for (cnt = 0, sum = 0., i = 0; i  n; i++, ix++)
if (*ix != NA_INTEGER) {cnt++; sum += *ix;}
else if (keepNA) {sum = NA_REAL; break;}
break;
case LGLSXP:
ix = LOGICAL(x) + n*j; 
for (cnt = 0, sum = 0., i = 0; i  n; i++, ix++)
if (*ix != NA_LOGICAL) {cnt++; sum += *ix;}
else if (keepNA) {sum = NA_REAL; break;}
break;
default:
/* we checked the type above, but be sure */
UNIMPLEMENTED_TYPEt(do_colsum, type);
}
if (OP == 1) {
if (cnt  0) sum /= cnt; else sum = NA_REAL;
}
REAL(ans)[j] = sum;
}


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Re: [Rd] sysdata.rda, namespaces and package dependencies

2011-08-30 Thread Duncan Murdoch

On 30/08/2011 11:27 AM, Hadley Wickham wrote:

  Your package is doing something weird, so I think it's you:  you are loading
  the munsell.map file via load.r in the top level of the package.  That's
  not a standard thing to do, and it's not being executed in the first case.

  Put that load statement into one of the files in the R directory and things
  should be fine.

I think that's a red-herring - load.r is for development and is never
run during usual package installation.  Or are you saying I need to
explicit load data stored in sysdata.rda within the package?



Sorry, I didn't realize you weren't executing that file.  (Should it be 
included in the tar?  That's a different issue...)


Lazy data is stored in a separate file that is loaded when 
library(munsell) is called.  It appears it isn't being loaded when you 
only use munsell::mnsl to load it but not attach it.  Certainly loading 
it from one of your .R files would work; I'm not sure if it is 
intentional that this is necessary or not.  Perhaps someone else will 
comment?


Duncan Murdoch

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Re: [Rd] sysdata.rda, namespaces and package dependencies

2011-08-30 Thread Uwe Ligges



On 30.08.2011 18:59, Duncan Murdoch wrote:

On 30/08/2011 11:27 AM, Hadley Wickham wrote:

 Your package is doing something weird, so I think it's you: you are
loading
 the munsell.map file via load.r in the top level of the package.
That's
 not a standard thing to do, and it's not being executed in the first
case.

 Put that load statement into one of the files in the R directory and
things
 should be fine.

I think that's a red-herring - load.r is for development and is never
run during usual package installation. Or are you saying I need to
explicit load data stored in sysdata.rda within the package?



Sorry, I didn't realize you weren't executing that file. (Should it be
included in the tar? That's a different issue...)

Lazy data is stored in a separate file that is loaded when
library(munsell) is called. It appears it isn't being loaded when you
only use munsell::mnsl to load it but not attach it. Certainly loading
it from one of your .R files would work; I'm not sure if it is
intentional that this is necessary or not. Perhaps someone else will
comment?


This is expected. The data object is not exported from the Namespace and 
hence not loaded if a reference to the Namespace is made without 
*attaching* the package. Hence data(..., package=...) is the way to go.


Uwe







Duncan Murdoch

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[Rd] Non-GPL C (or R) inside of a package

2011-08-30 Thread Jeffrey Ryan
R-devel,

I am interested in creating a package that requires non-GPL'd (commercial) C
code to work.  In essence it is a single .c file with no use of R headers
(all .C callable functions).  For example's sake:

  1 #include stdio.h
  2
  3 void test (int *a) {
  4   *a = 101;
  5 }

The package isn't destined for CRAN, and I realize that this isn't R-legal,
but looking for some expert advice from anyone else who may have encountered
this previously.

The question is whether or not one can distribute code that has multiple
licenses (.c or individual .R files), including some that are not
GPL-compatible, as a tar.gz (or binary) file.  i.e., does the packaging
process [R CMD ***] cause everything to become GPL, as we are using R itself
to build the package?

I can of course provide the C libs in this case as a separate install, but
that adds complexity to the overall build and install process.

Thanks,
Jeff

-- 
Jeffrey Ryan
jeffrey.r...@lemnica.com

www.lemnica.com
www.esotericR.com

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Re: [Rd] sysdata.rda, namespaces and package dependencies

2011-08-30 Thread Hadley Wickham
 Lazy data is stored in a separate file that is loaded when
 library(munsell) is called. It appears it isn't being loaded when you
 only use munsell::mnsl to load it but not attach it. Certainly loading
 it from one of your .R files would work; I'm not sure if it is
 intentional that this is necessary or not. Perhaps someone else will
 comment?

 This is expected. The data object is not exported from the Namespace and
 hence not loaded if a reference to the Namespace is made without *attaching*
 the package. Hence data(..., package=...) is the way to go.

So how should I include package local data?  The dataset is only used
internally by munsell functions (it's basically a big lookup table)
and should not be available to the user - i.e. it should not be
exported.  This, I thought, was the purpose of sysdata.rda.

Hadley

-- 
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/

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Re: [Rd] sysdata.rda, namespaces and package dependencies

2011-08-30 Thread Uwe Ligges



On 30.08.2011 19:52, Hadley Wickham wrote:

Lazy data is stored in a separate file that is loaded when
library(munsell) is called. It appears it isn't being loaded when you
only use munsell::mnsl to load it but not attach it. Certainly loading
it from one of your .R files would work; I'm not sure if it is
intentional that this is necessary or not. Perhaps someone else will
comment?


This is expected. The data object is not exported from the Namespace and
hence not loaded if a reference to the Namespace is made without *attaching*
the package. Hence data(..., package=...) is the way to go.


So how should I include package local data?  The dataset is only used
internally by munsell functions (it's basically a big lookup table)
and should not be available to the user - i.e. it should not be
exported.  This, I thought, was the purpose of sysdata.rda.

Hadley



A
Now I understand you are referring to the special name sysdata.rda 
that is not to be loaded via data() - I thought you were talking about 
the regular data including process.
That works fine for me as well and then this special data are available 
when the Namespace is loaded already. Have you put that file into 
package/R rather than package/data? Which R version?


Uwe

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Re: [Rd] Non-GPL C (or R) inside of a package

2011-08-30 Thread Duncan Murdoch

On 30/08/2011 1:50 PM, Jeffrey Ryan wrote:

R-devel,

I am interested in creating a package that requires non-GPL'd (commercial) C
code to work.  In essence it is a single .c file with no use of R headers
(all .C callable functions).  For example's sake:

   1 #includestdio.h
   2
   3 void test (int *a) {
   4   *a = 101;
   5 }

The package isn't destined for CRAN, and I realize that this isn't R-legal,
but looking for some expert advice from anyone else who may have encountered
this previously.

The question is whether or not one can distribute code that has multiple
licenses (.c or individual .R files), including some that are not
GPL-compatible, as a tar.gz (or binary) file.  i.e., does the packaging
process [R CMD ***] cause everything to become GPL, as we are using R itself
to build the package?

I can only say that the answer to the last question is no:  the author 
gets to choose the license for what s/he wrote.  The fact that you used 
R to package it is irrelevant.  (Some extremists will disagree, and say 
that because your package is intended to link to R, it must be 
licensed compatibly with the GPL if you distribute it.  I don't think 
that's true.)


If you are intending to distribute this file you are putting together, 
you'll probably want to consult someone who knows the legalities as to 
whether you can legally link to the commercial library...


Duncan Murdoch


I can of course provide the C libs in this case as a separate install, but
that adds complexity to the overall build and install process.

Thanks,
Jeff



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Re: [Rd] Non-GPL C (or R) inside of a package

2011-08-30 Thread Prof Brian Ripley

On Tue, 30 Aug 2011, Duncan Murdoch wrote:


On 30/08/2011 1:50 PM, Jeffrey Ryan wrote:

R-devel,

I am interested in creating a package that requires non-GPL'd 
(commercial) C code to work.  In essence it is a single .c file 
with no use of R headers (all .C callable functions).  For 
example's sake:


   1 #includestdio.h
   2
   3 void test (int *a) {
   4   *a = 101;
   5 }

The package isn't destined for CRAN, and I realize that this isn't 
R-legal, but looking for some expert advice from anyone else who 
may have encountered this previously.


The question is whether or not one can distribute code that has 
multiple licenses (.c or individual .R files), including some that 
are not GPL-compatible, as a tar.gz (or binary) file.  i.e., does 
the packaging process [R CMD ***] cause everything to become GPL, 
as we are using R itself to build the package?


I can only say that the answer to the last question is no:  the author gets 
to choose the license for what s/he wrote.  The fact that you used R to 
package it is irrelevant.  (Some extremists will disagree, and say that 
because your package is intended to link to R, it must be licensed 
compatibly with the GPL if you distribute it.  I don't think that's true.)


If no distribution is involved, the conditions under which the tarball 
can be distributed is not relevant.


As e.g. GNU tar is itself under GPL, using R to do the packaging is no 
different in principle to using GNU tar to do so and I've never heard 
anyone argue that using GNU tar affects the licence of the tarball.


I don't think that is the same issue as distributing non-GPLed code 
for use with R.  In the latter case the issue is what 'link to' 
actually entails, and one source of advice is the GPL FAQs.  E.g.

http://www.gnu.org/licenses/old-licenses/gpl-2.0-faq.html
http://www.gnu.org/licenses/gpl-faq.html

If you are intending to distribute this file you are putting together, you'll 
probably want to consult someone who knows the legalities as to whether you 
can legally link to the commercial library...






Duncan Murdoch


I can of course provide the C libs in this case as a separate install, but
that adds complexity to the overall build and install process.

Thanks,
Jeff



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University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
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Re: [Rd] Out-of-date manual or small bug in R CMD check?

2011-08-30 Thread William Dunlap

 -Original Message-
 From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On 
 Behalf Of Duncan Murdoch
 Sent: Monday, August 29, 2011 5:30 PM
 To: Gabriel Becker
 Cc: r-devel@r-project.org
 Subject: Re: [Rd] Out-of-date manual or small bug in R CMD check?
 
 On 11-08-29 6:37 PM, Gabriel Becker wrote:
  Hey all,
 
  I get a warning about an unsupported file type in the data directory during
  R CMD check (for R 2.13.1) if I use the save function to create an Rdata,
  but if I save the same object to a .rda file, no warning.
 
  Section 1.1.5 (pg 11 of the pdf) of the Writing R Extensions manual (2.13.1)
  appears to say that .Rdata files should be fine:
 
   Data files can have one of three types as indicated by their extension:
  plain R code ('.R' or
  '.r'), tables ('.tab', '.txt', or '.csv', see ?data for the file formats,
  and note that '.csv' is not
  the standard14 CSV format), or save() images ('.RData' or '.rda'). 
 
  Am I misunderstanding some difference between .rda and .Rdata files in terms
  of the save calls, or should R CMD check and the extensions manual agree on
  this?
 
 .RData and .Rdata aren't the same.

Should that paragraph say that capitalization matters and that the following
file name extensions are recognized
  TXT
  txt
  CSV
  csv
  tab
  r
  R
  rdata
  RData
  rda
(and that others that vary only by case, such as TAB, Rdata and Rda, are not)?

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com

 
 Duncan Murdoch
 
 
  Thanks for all your hard work.
  ~G
 
  SessionInfo:
 
  R version 2.13.1 (2011-07-08)
  Platform: x86_64-pc-linux-gnu (64-bit)
 
  locale:
[1] LC_CTYPE=en_US.utf8   LC_NUMERIC=C
[3] LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8   LC_NAME=C
[9] LC_ADDRESS=C  LC_TELEPHONE=C
  [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
 
  attached base packages:
  [1] grid  stats graphics  grDevices utils datasets  methods
  [8] base
 
  other attached packages:
  [1] gridSVG_0.5-10  ProteinVis_0.4  latticeExtra_0.6-18
  [4] RColorBrewer_1.0-2  lattice_0.19-33
 
 
 
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[Rd] Possible to read R_StringHash from a package?

2011-08-30 Thread Matthew Dowle
Is there any way to look at R_StringHash from a package? I've read
R-Ints 1.16.1 Hiding C entry points and seen that R_StringHash is
declared as extern0 in Defn.h. So it seems the answer is no.

Thanks,
Matthew

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Re: [Rd] sysdata.rda, namespaces and package dependencies

2011-08-30 Thread Hadley Wickham
 That works fine for me as well and then this special data are available when
 the Namespace is loaded already. Have you put that file into package/R
 rather than package/data? Which R version?

Yes, sysdata.rda is in package/R - source code available here:
https://github.com/cwickham/munsell/tree/master/R

I'm running 2.13.1 (on a mac)

Hadley


-- 
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/

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