[Rd] make.packages.html
In R version 2.10.0 Patched (2009-11-15 r50445) on Windows Vista
upon issuing help.start() and clicking on Packages I get this.
Packages in C:\Users\Gabor\Documents\R\win-library\2.10
C:\Users\Gabor\Documents/R/win-library/2.10/AER/DESCRIPTION -- Title
is missing --
C:\Users\Gabor\Documents/R/win-library/2.10/akima/DESCRIPTION -- Title
is missing --
C:\Users\Gabor\Documents/R/win-library/2.10/car/DESCRIPTION -- Title
is missing --
C:\Users\Gabor\Documents/R/win-library/2.10/caroline/DESCRIPTION --
Title is missing --
...
Looking at make.packages.html in utils, this code:
for (lib in lib.loc) {
pg - Sys.glob(file.path(lib, *, DESCRIPTION))
pkgs[[lib]] - sort(sub(paste(lib, ([^/]*), DESCRIPTION$,
sep = /), \\1, pg))
}
has the problem that lib can contain regular expression characters but
is used in the pattern of sub. This could be changed to the following
which does not use lib in any pattern. Only the pkgs[[lib]]-
statement is changed relative to the original:
for (lib in lib.loc) {
pg - Sys.glob(file.path(lib, *, DESCRIPTION))
pkgs[[lib]] - sort(sub(.*[\\/], , sub(.DESCRIPTION$, , pg)))
}
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Re: [Rd] make.packages.html
On 17/11/2009 5:33 AM, Gabor Grothendieck wrote:
In R version 2.10.0 Patched (2009-11-15 r50445) on Windows Vista
upon issuing help.start() and clicking on Packages I get this.
Packages in C:\Users\Gabor\Documents\R\win-library\2.10
C:\Users\Gabor\Documents/R/win-library/2.10/AER/DESCRIPTION -- Title
is missing --
C:\Users\Gabor\Documents/R/win-library/2.10/akima/DESCRIPTION -- Title
is missing --
C:\Users\Gabor\Documents/R/win-library/2.10/car/DESCRIPTION -- Title
is missing --
C:\Users\Gabor\Documents/R/win-library/2.10/caroline/DESCRIPTION --
Title is missing --
...
Looking at make.packages.html in utils, this code:
for (lib in lib.loc) {
pg - Sys.glob(file.path(lib, *, DESCRIPTION))
pkgs[[lib]] - sort(sub(paste(lib, ([^/]*), DESCRIPTION$,
sep = /), \\1, pg))
}
has the problem that lib can contain regular expression characters but
is used in the pattern of sub. This could be changed to the following
which does not use lib in any pattern. Only the pkgs[[lib]]-
statement is changed relative to the original:
for (lib in lib.loc) {
pg - Sys.glob(file.path(lib, *, DESCRIPTION))
pkgs[[lib]] - sort(sub(.*[\\/], , sub(.DESCRIPTION$, , pg)))
}
Thanks, I'll take a look.
Duncan Murdoch
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Re: [Rd] make.packages.html
On 17/11/2009 5:33 AM, Gabor Grothendieck wrote:
In R version 2.10.0 Patched (2009-11-15 r50445) on Windows Vista
upon issuing help.start() and clicking on Packages I get this.
Packages in C:\Users\Gabor\Documents\R\win-library\2.10
C:\Users\Gabor\Documents/R/win-library/2.10/AER/DESCRIPTION -- Title
is missing --
C:\Users\Gabor\Documents/R/win-library/2.10/akima/DESCRIPTION -- Title
is missing --
C:\Users\Gabor\Documents/R/win-library/2.10/car/DESCRIPTION -- Title
is missing --
C:\Users\Gabor\Documents/R/win-library/2.10/caroline/DESCRIPTION --
Title is missing --
...
Looking at make.packages.html in utils, this code:
for (lib in lib.loc) {
pg - Sys.glob(file.path(lib, *, DESCRIPTION))
pkgs[[lib]] - sort(sub(paste(lib, ([^/]*), DESCRIPTION$,
sep = /), \\1, pg))
}
has the problem that lib can contain regular expression characters but
is used in the pattern of sub. This could be changed to the following
which does not use lib in any pattern. Only the pkgs[[lib]]-
statement is changed relative to the original:
for (lib in lib.loc) {
pg - Sys.glob(file.path(lib, *, DESCRIPTION))
pkgs[[lib]] - sort(sub(.*[\\/], , sub(.DESCRIPTION$, , pg)))
}
I've committed your patch to R-devel and R-patched now. Thanks!
Duncan Murdoch
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Re: [Rd] How to generate dependency file that can be used by gnu make?
This may not easy to do, when the filename are not hard coded strings.
For example, the variable 'filename' is a vector of strings.
for (i in 1:length(filename)){
do something...
save(,file=filename[i])
}
On Mon, Nov 16, 2009 at 11:33 PM, Linlin Yan yanlinli...@gmail.com wrote:
I don't think this function is same as gcc's option -MM. Because gcc
checks pre-compile command #include, in which the filename can be
fetched definitely. But in your scenario, the filename may be from
some variables, which can not be determined by the R script only.
Maybe you can write a tool by yourself to parse the R syntax to
resolve your problem.
On Tue, Nov 17, 2009 at 11:51 AM, Peng Yu pengyu...@gmail.com wrote:
On Sun, Nov 15, 2009 at 8:45 PM, Peng Yu pengyu...@gmail.com wrote:
gcc has options like -MM, which can generate the dependence files for
a C/C++ file that I can be used by gnu make. I'm wondering if there is
a tool that can generate dependence file for an R script.
For example, I have an R script test.R
#test.R
load('input.RData')
save.image('output.RData')
I want to generate a dependence file like the following. Is there a
tool to do so?
output.RData:test.R input.RData
Is there a way to automatically generate the output files that depends
on an R script and the input files and sourced files that are depended
by an R script? I don't see this option in R. But I wish this can be
implemented in future version of R.
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Re: [Rd] How to generate dependency file that can be used by gnu make?
On 11/17/09 5:02 AM, Peng Yu wrote:
This may not easy to do, when the filename are not hard coded strings.
For example, the variable 'filename' is a vector of strings.
for (i in 1:length(filename)){
do something...
save(,file=filename[i])
}
That's right. I don't think there is a feasible general solution. You
might have more success with a convention-based approach for your
scripts that would allow a simple parser to identify output files by
name convention, for example.
+ seth
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[Rd] Codoc mismatches
I have a function:
source_dir - function(path, pattern = \\.[rR]$, chdir = TRUE) ...
documented with
...
\usage{source_dir(path, pattern=\\.[rR]$, chdir=TRUE)}
...
But I get
Codoc mismatches from documentation object 'source_dir':
source_dir
Code: function(path, pattern = \\.[rR]$, chdir = TRUE)
Docs: function(path, pattern = \.[rR]$, chdir = TRUE)
Mismatches in argument default values:
Name: 'pattern' Code: \\.[rR]$ Docs: \.[rR]$
Is this a bug, or do I need
\usage{source_dir(path, pattern=.[rR]$, chdir=TRUE)}
?
Hadley
--
http://had.co.nz/
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Re: [Rd] R crash with intToUtf8 on huge vectors (PR#14068)
On 11/16/2009 8:10 AM, g.russ...@eos-solutions.com wrote: Full_Name: George Russell Version: 2.10.0 OS: Windows XP Professional Version 2002 Service Pack 2 Submission from: (NULL) (217.111.3.131) Typing the following command into R --vanilla causes R to crash: k - intToUtf8(rep(1e3,1e7)) Brian Ripley has tracked this one down and a fix should appear shortly. The intToUtf8 code was written for reasonably small conversions, and it overflowed the stack when it tried to produce a 20 megabyte string there. Do you have a real application that works with such large strings? Duncan Murdoch This is the output of sessionInfo(): R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] RODBC_1.3-1 Many thanks for your help and best wishes, George Russell __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R crash with intToUtf8 on huge vectors (PR#14068)
Basically you have exceeded a resource limit, and Windows has not handled that gracefully (other OSes do in your example). You are trying to create a single 20Mb string and no one envisaged anyone wanting to do that (nor that Windows would not fail gracefully, although generically that comes as no real surprise)). We'll change the method to cope with very large strings (more slowly), but perhaps you could explain the real-world problem that needs 20Mb strings to be produced from integer representations of Unicode points? On Mon, 16 Nov 2009, g.russ...@eos-solutions.com wrote: Full_Name: George Russell Version: 2.10.0 OS: Windows XP Professional Version 2002 Service Pack 2 Submission from: (NULL) (217.111.3.131) Typing the following command into R --vanilla causes R to crash: k - intToUtf8(rep(1e3,1e7)) This is the output of sessionInfo(): R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] RODBC_1.3-1 Many thanks for your help and best wishes, George Russell __ 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] make.packages.html
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Duncan Murdoch
Sent: Tuesday, November 17, 2009 2:50 AM
To: Gabor Grothendieck
Cc: r-devel@r-project.org
Subject: Re: [Rd] make.packages.html
On 17/11/2009 5:33 AM, Gabor Grothendieck wrote:
In R version 2.10.0 Patched (2009-11-15 r50445) on Windows Vista
upon issuing help.start() and clicking on Packages I get this.
Packages in C:\Users\Gabor\Documents\R\win-library\2.10
C:\Users\Gabor\Documents/R/win-library/2.10/AER/DESCRIPTION -- Title
is missing --
C:\Users\Gabor\Documents/R/win-library/2.10/akima/DESCRIPTION -- Title
is missing --
C:\Users\Gabor\Documents/R/win-library/2.10/car/DESCRIPTION -- Title
is missing --
C:\Users\Gabor\Documents/R/win-library/2.10/caroline/DESCRIPTION --
Title is missing --
...
Looking at make.packages.html in utils, this code:
for (lib in lib.loc) {
pg - Sys.glob(file.path(lib, *, DESCRIPTION))
pkgs[[lib]] - sort(sub(paste(lib, ([^/]*),
DESCRIPTION$,
sep = /), \\1, pg))
}
has the problem that lib can contain regular expression
characters but
is used in the pattern of sub. This could be changed to
the following
which does not use lib in any pattern. Only the pkgs[[lib]]-
statement is changed relative to the original:
for (lib in lib.loc) {
pg - Sys.glob(file.path(lib, *, DESCRIPTION))
pkgs[[lib]] - sort(sub(.*[\\/], ,
sub(.DESCRIPTION$, , pg)))
}
Thanks, I'll take a look.
Hadley Wickham asked last week about a function that escaped
all the regular-expression special characters in a
string, so one could use gsub with fixed=TRUE,
and I suggested
asFixedRegex - function(pattern) {
gsub(([][^${}().?*+|\\]), \\1, pattern)
}
(I left out the | in the original mail). asFixedRegex()
could be used to fix this problem by changing 'lib' to
'asFixedRegex(lib)' in the offending call to sub
sub(paste(asFixedRegex(lib), ([^/]*), DESCRIPTION$, sep = /),
\\1, pg)
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
Duncan Murdoch
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Re: [Rd] Codoc mismatches
You need . See R-exts 2.14.2. It also confused me the other day.
Regards,
Yihui
--
Yihui Xie xieyi...@gmail.com
Phone: 515-294-6609 Web: http://yihui.name
Department of Statistics, Iowa State University
3211 Snedecor Hall, Ames, IA
On Tue, Nov 17, 2009 at 9:26 AM, Hadley Wickham had...@rice.edu wrote:
I have a function:
source_dir - function(path, pattern = \\.[rR]$, chdir = TRUE) ...
documented with
...
\usage{source_dir(path, pattern=\\.[rR]$, chdir=TRUE)}
...
But I get
Codoc mismatches from documentation object 'source_dir':
source_dir
Code: function(path, pattern = \\.[rR]$, chdir = TRUE)
Docs: function(path, pattern = \.[rR]$, chdir = TRUE)
Mismatches in argument default values:
Name: 'pattern' Code: \\.[rR]$ Docs: \.[rR]$
Is this a bug, or do I need
\usage{source_dir(path, pattern=.[rR]$, chdir=TRUE)}
?
Hadley
--
http://had.co.nz/
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[Rd] R_NilValue and segfault.
Hello.
I've been trying to wrap up the R_NilValue into OCaml-R. I nevertheless
get a segfault.
As I gathered, R_NilValue is declared in Rinternals.h:
/* Special Values */
LibExtern SEXP R_NilValue; /* The nil object */
LibExtern SEXP R_UnboundValue; /* Unbound marker */
LibExtern SEXP R_MissingArg; /* Missing argument marker */
So, in my r_data.c file, I have:
-1- an #include directive.
#include Rinternals.h
-2- the function wrapping R data in OCaml data
CAMLprim value Val_sexp (SEXP sexp)
{
CAMLparam0();
CAMLlocal1(result);
result = caml_alloc(1, Abstract_tag);
Field(result, 0) = (value) sexp;
/* Do not use Val_long in the above statement,
as it will drop the top bit. See mlvalues.h. */
CAMLreturn(result);
}
and a function taking no argument (in the sense of OCaml), and returning
an OCaml object encapsulating a pointer which is R_NilValue. (R_NilValue
is already a pointer, so we just copy it).
/* The NULL constant in R... */
CAMLprim value r_null (value unit) {
CAMLparam1(unit);
CAMLreturn(Val_sexp(R_NilValue));
}
OCaml code is straightforward:
external null_creator : unit - sexp = r_null
let null = null_creator ()
And I get a segfault:
Objective Caml version 3.11.1
# R.sexptype (R.sexp 1);;
- : R.sexptype = R.RealSxp
# R.sexptype Quantmod.getSymbols;;
- : R.sexptype = R.PromSxp
The two above are fine, but inspecting the type of R.null gives me a
segfault.
# R.sexptype R.null;;
/usr/bin/ocaml-batteries: line 2: 3723 Erreur de segmentation
/usr/lib/ocaml/batteries/toplevel.top /usr/lib/ocaml/batteries/top.ml $@
Please tell me if there's anything obvious which causes this. There's a
lot of conditional compilation directives in Rinternals.h, and I'm
wondering whether or not that might be an issue.
All the best,
--
Guillaume Yziquel
http://yziquel.homelinux.org/
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Re: [Rd] R_NilValue and segfault.
Guillaume Yziquel a écrit : Hello. I've been trying to wrap up the R_NilValue into OCaml-R. I nevertheless get a segfault. Is the value of R_NilValue (I mean the address in the R_NilValue pointer located in the uninitialized data section - i.e. the BSS section) set up *after* the init function is called? -- Guillaume Yziquel http://yziquel.homelinux.org/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R_NilValue and segfault.
Guillaume Yziquel a écrit : Guillaume Yziquel a écrit : Hello. I've been trying to wrap up the R_NilValue into OCaml-R. I nevertheless get a segfault. Is the value of R_NilValue (I mean the address in the R_NilValue pointer located in the uninitialized data section - i.e. the BSS section) set up *after* the init function is called? I mean: after the Rf_initEmbeddedR is called? I Objective Caml is really static. Which means that if I declare R.null to be R_NilValue, it will take the value of the pointer before Rf_initEmbeddedR is executed. And it would be garbage. That would perhaps be my issue. Could someone confirm? All the best, -- Guillaume Yziquel http://yziquel.homelinux.org/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
