Re: [Rd] Double HTML encoding in R Bug Tracking Submission form (PR#11517)

2008-05-25 Thread Peter Dalgaard

[EMAIL PROTECTED] wrote:
The "New Bug Report" form available from http://bugs.r-project.org/ 
appears to double encode the HTML of the "body" text area of the form.


This behaviour can be seen in submission ID # 11515, where (as an 
example) "Δ" is converted to "Δ" in the browser view or 
"Δ" in the HTML source code. Conversion to "Δ" in the HTML 
source is sufficient to render "Δ" in the browser output.


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Well, the repository handles emails, and the report form sends mail to 
the bug repository.


The report form sends HTML codes without any indication that it is doing 
so, so the codes get rendered in the browser view. This latter part is 
actually correct behaviour since the alternative is to mangle all 
ampersands. So the main bug is that the report form is not mail-encoding 
the contents if non-ASCII.


*However*, even with properly encoded mails, the browser view will not 
interpret the encoding, which is particularly annoying with 
quoted-printable (which uses the equal sign as an escape character and 
changes = to =3D). Also, see what happens with my signature which has a 
UTF-8 character inside.


All in all, the whole mess indicates that the bug repository software is 
dying. It has long since been abandoned by its original author and it 
makes no sense for the R Core Team to make major changes to its 
internals. We've been wanting to move to something more mainstream for 
quite a while, but it takes some effort to find out how to move all the 
old pending and resolved reports across.


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[Rd] Listing all possible samples of Size two form Large Population

2008-05-25 Thread Nadeem Shafique
Respected All,

I need some efficient program or package to draw all possible samples
of size two without replacement. I am using "combinat" package to list
all possible samples but it hangs my computer for larger populations
say 10,000 (i.e. 49995000 all possible samples). I wish to even work
for larger populations then this and replicate this procedure for many
times. Kindly can anyone figure out the possibilities and let me know.

Best Regards,

Nadeem Shafique Butt

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[Rd] Double HTML encoding in R Bug Tracking Submission form (PR#11517)

2008-05-25 Thread mwtoews
The "New Bug Report" form available from http://bugs.r-project.org/ 
appears to double encode the HTML of the "body" text area of the form.

This behaviour can be seen in submission ID # 11515, where (as an 
example) "Δ" is converted to "Δ" in the browser view or 
"Δ" in the HTML source code. Conversion to "Δ" in the HTML 
source is sufficient to render "Δ" in the browser output.

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[Rd] (PR#11482)

2008-05-25 Thread gabraham
You didn't mention on R-help that the bug was already fixed in 2.7.0 
patched, otherwise I wouldn't have bothered with a bug report.

-- 
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Dept. CSSE and NICTA
The University of Melbourne
Parkville 3010, Victoria, Australia
email: [EMAIL PROTECTED]
web: http://www.csse.unimelb.edu.au/~gabraham

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[Rd] Using unicode with sprintf or paste in Windows (PR#11515)

2008-05-25 Thread mwtoews
Full_Name: Michael Toews
Version: 2.7.0
OS: Windows XP SP2
Submission from: (NULL) (24.80.163.230)


Using Unicode characters in Windows works with static strings (as of R 2.7.0),
however fails when used with sprintf() or paste(). For example, on R 2.7.0 for
Windows XP (SP2):

Static string (works, showing Greek Delta character):
> print("\u0394Q = 2.2 L/s")
[1] "ΔQ = 2.2 L/s"

However, when I use paste() or sprintf(), the Unicodeness is lost:
> paste("\u0394Q =",round(1.2345,3),"L/s")
[1] "Q = 1.234 L/s"
> sprintf("\u0394Q = %.3f L/s",1.2345)
[1] "Q = 1.234 L/s"


I have also tested this with R 2.7.0 for Linux, which yields the following:
> print("\u0394Q = 2.2 L/s")
[1] "ΔQ = 2.2 L/s"
> paste("\u0394Q =",round(1.2345,3),"L/s")
[1] "ΔQ = 1.234 L/s"
> sprintf("\u0394Q = %.3f L/s",1.2345)
[1] "ΔQ = 1.234 L/s"

(Note: this was posted on R-help with no replies:
https://stat.ethz.ch/pipermail/r-help/2008-May/162815.html )

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[Rd] format.factor (PR#11512)

2008-05-25 Thread oehl_list
Dear all,

differing from the standard behaviour of 'format' the current (2.7.0) 
'format.factor' destroys attributes like 'dim' and 'dimnames'. This 
unfortunately breaks some general code in the new package 'ff' for large 
file-based data which will support vectors and arrays of atomic and factors. 

It would be nice if you could include the following fix in the next release of 
R. 

Kind regards

Jens Oehlschlägel

format.factor <-
function (x, ...){
  a <- attributes(x)
  a$class <- NULL
  a$levels <- NULL
  x <- as.character(x)
  attributes(x) <- a
  format(x, ...)
}


>   x <- factor(c("aa",letters[-1]))
>   dim(x) <- c(13,2)
>   format(x, justify="right")
 [1] "aa" " b" " c" " d" " e" " f" " g" " h" " i" " j" " k" " l" " m" " n" " o" 
" p" " q" " r" " s" " t" " u" " v" " w" " x" " y" " z"
> 
>   format.factor <-
+   function (x, ...){
+ a <- attributes(x)
+ a$class <- NULL
+ a$levels <- NULL
+ x <- as.character(x)
+ attributes(x) <- a
+ format(x, ...)
+   }
> 
>   format(x, justify="right")
  [,1] [,2]
 [1,] "aa" " n"
 [2,] " b" " o"
 [3,] " c" " p"
 [4,] " d" " q"
 [5,] " e" " r"
 [6,] " f" " s"
 [7,] " g" " t"
 [8,] " h" " u"
 [9,] " i" " v"
[10,] " j" " w"
[11,] " k" " x"
[12,] " l" " y"
[13,] " m" " z"

> version
   _   
platform   i386-pc-mingw32 
arch   i386
os mingw32 
system i386, mingw32   
status 
major  2   
minor  7.0 
year   2008
month  04  
day22  
svn rev45424   
language   R   
version.string R version 2.7.0 (2008-04-22)

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Re: [Rd] Macintosh Transperancy (PR#11511)

2008-05-25 Thread Prof Brian Ripley
Bradley -- please learn the difference between 'transparent' and 
'semi-transparent'/'translucent'.  Your statements only begin to make 
sense for partially opaque colours.  Furthermore, there was a bug in the 
handling of (fully) transparent colours for these pch's what has been 
fixed in R-patched.


Also, the FAQ does ask you to make a bug report _only_ if you 'know for 
certain' what should happen, and here you are saying you would like to be 
able to do something different.  (It also discusses how to make 'wishlist' 
proposals, but you did not follow that and such proposals need to be 
unambiguously documented.)  You had better also 'know for certain' what 
does actually happen with current R versions.


There are several ways to handle semi-transparency, and Paul Murrell and I 
have debated which is the correct one to use.  In the case of pch=21:25 
where there may be two semi-transparent colours to paint, it is pretty 
clear that sensible people expect the two colours to be painted separately 
(they need not even have the same opacity).  If you don't want the border 
to be painted, make it transparent (and use R-patched or later).


Where the issue is less clear-cut is in pch=16 or 19, where the disc does 
have a stroked border of the same colour.  There devices do differ.

So if I do

plot(1, type="n")
points(1,1,pch=16, cex=10, lwd=3, col="#0030")

on pdf() I get a disc of uniform colour and AFAIR on all other devices 
which support transparency give a darker border.  The point being that if 
we paint a fill and then a border in the same semi-transparent colour, 
should the overlap be painted once or twice?  I've not yet convinced Paul 
that we should take a position on what should happen here (and the use of 
anti-aliasing on lines or even fills means that what actually happens on 
some devices is more complicated still--and more complicated again on 
monitors such as mine which have hardware sharpening).


However, if you care you can use pch=21 with a transparent 'col' to 
achieve a uniform disc on all devices.



On Sat, 24 May 2008, Simon Urbanek wrote:


Bradley,

On May 24, 2008, at 9:07 PM, Bradley Vance wrote:

	The bug is that the point that's being plotted is a single point, not 
a combination of two points, one that's just the outline, and one that's 
just the fill.  It also doesn't look like we'd expect when you're debugging 
a plot.  For example, let's say I create a plot, and notice that I can't 
see some of the points (due to other points being drawn on top of them). 
So I decide to make them transparent, so you can see where points over-lay 
each other, and the relative size/colors/etc of the over-layed points. 
Now, rather than just changing the opacity of the points/colors I see, I'm 
adding in another color to each point where outline and background meet, 
making the plot more confusing than it needs to be...
	In looking at the documentation for bg in points (plot says to look 
at points for bg) it says

bgbackground (fill) color for the open plot symbols given by pch=21:25.
and the way it is now, the color is not a fill (ie - inside the lines) - 
it's super-imposed over part of the line.


I think you're still missing the point - it is the fill. I suspect you're 
misunderstanding the effect of using semi-transparent strokes. Moreover I get 
*exactly* the same result using X11 (both Mac *and* Linux) as well as other 
devices (PDF etc.). If you see anything else then *that* is a bug.


A point is represented by a shape (path) which is filled and then drawn (line 
stroke). As I was trying to explain earlier the effect is that half of the 
line is in the filled area. Imagine a rectangle (0,0)-(1,1). When you fill 
it, you're filling strictly the area between 0 and 1 (in both x and y). 
However, when you strike let's say the line (0,0)-(1,0) with the width 0.25, 
you are filling the area (0,-0.25)-(1,+0.25) which means that half the line 
is outside (y<0) the filled are and another half is inside (y>=0). Given the 
alpha-blending mechanics [target=alpha*color + (1-alpha)*old] it implies that 
if the fill color is different from the background color and the line is not 
opaque, you get different color outside and inside the rectangle. You can 
verify that this is true for all devices that support alpha blending. This is 
how it works and is supposed to be, that's not a bug.



	Also, there's the fact that it does something different on different 
systems.  When I do the same thing at work on a Linux box (we don't have 
R.2.7 yet, we use mostly R2.4 but I've tried it on R2.6,


Well, 2.6 didn't have alpha support in X11 AFAIR, so I have no idea what you 
are trying to compare there ...



and we don't have Quartz, but I did output to PDF), it looks like a single 
point whose colors were made transparent, and not a point made of two 
overlapping transparent parts.
	As I implied in my original ticket, I'd like to be able to choose 
whether to have it look the way it does now on the