On Fri, 10 Jun 2005 [EMAIL PROTECTED] wrote:
> hello bug fixers
>
> i think this bug is probably mentioned before but i couldn't find the
> answer to it on google.
> i have to build R from the source files ( on a mac os x system )
> because i need the python R interface too work. for this too happ
On Mon, 13 Jun 2005, Gordon K Smyth wrote:
> This is just a note that R would get a lot more citations if the
> recommended citation was an article in a recognised journal or from a
> recognised publisher.
>
This is unfortunately true, but R is *not* an article or a book, it is a
piece of soft
Online registration for DSC 2005 in Seattle, August 13-14 is now open. See
the conference web page at
http://depts.washington.edu//dsc2005/
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
Persons conversant with W3C standards would have noticed too many // in the URL
quoted in my previous message. The correct conference page URL is
http://depts.washington.edu/dsc2005
-thomas
On Mon, 13 Jun 2005, Thomas Lumley wrote:
>
> Online registration for DSC 2005 in S
This was supposed to be fixed in 2.1.1 -- which version are you using?
-thomas
On Tue, 21 Jun 2005, Martin Maechler wrote:
> We have been using Redhat Enterprise 4, on some of our Linux
> clients for a while,
> and Christoph has just found that opening an R device for a file
> without w
On Tue, 21 Jun 2005, Martin Maechler wrote:
>>>>>> "TL" == Thomas Lumley <[EMAIL PROTECTED]>
>>>>>> on Tue, 21 Jun 2005 09:59:31 -0700 (PDT) writes:
>
>TL> This was supposed to be fixed in 2.1.1 -- which version are you u
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>
Thomas Lumley Assoc. Professor, Biostatistics
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On Wed, 6 Jul 2005, [iso-8859-1] Marie-Hélène Ouellette wrote:
Dear Dr. Ripley,
Or possibly other people on the list.
I'm using the R v1.11 on Macintoch
Unlikely. There is no R v1.11, and R 1.1.1 (following the most common
misspelling) wasn't available for the Mac.
On Wed, 6 Jul 2005, [iso-8859-1] Marie-H?l?ne Ouellette wrote:
And try to use the function:
> K_MEANSR(tab,centers=c(2,4))
[1] "AA"
[1] "AAA"
[1] "A"
[1] "B"
Error in .C("K_MEANSC", xrows = as.integer(xrows), xcols =
as.integer(xcols), :
"C" function name not in load table
Hmm. Stra
ing allocString.
-thomas
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On Mon, 1 Aug 2005, Gavin Simpson wrote:
> R-devel compiles without error (same set of flags as above) but fails
> make check-all in p-r-random-tests.R - the relevant section of p-r-
> random-tests.Rout.fail is:
>
> ...
>> dkwtest("norm")
> norm() PASSED
> [1] TRUE
>> dkwtest("norm",mean = 5,sd = 3
s
> or
>
>> x=.04
>> x
> [1] 0.04
>> y=.2*.2
>> y
> [1] 0.04
>> y==x
> [1] FALSE
>
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On Tue, 16 Aug 2005, Paul Mosquin wrote:
> I guess that I expect R to act pretty much as C or C++ would do if I were to
> program the same code. It's a bit of a surprise that assignment of
> rationals, well within precision, followed by multiplication leading to a
> result well within precision
1st Qu.Median Mean 3rd Qu. Max.
> ## -12.430-2.431 9.569 57.570 65120.000
> ## kk= 4
> ##Min. 1st Qu.Median Mean 3rd Qu. Max.
> ## -12.430-2.431 9.569 238.70057.570 65120.000
> ## kk= 5
> ##
On Mon, 29 Aug 2005, Harris, Michael (NIH/NCI) [E] wrote:
>
> I am getting a compile warning when building R from source. I am building
> on a AMD64 Opteron system with gcc (GCC) 3.3.3 (SuSE Linux)
>
> The warning is:
>
>unique.c: In function `cshash':
>
> unique.c:1146: warning: cas
On Tue, 31 Aug 2005, Peter Dalgaard wrote:
> Well, did you try running under a debugger?
>
> R -d gdb
>
> then "bt" after the segfault. (Make sure that things are compiled with
> -g option)
It would also be worth renaming the the function -- while I don't see
exactly how it could be causing the
On Fri, 2 Sep 2005, Martin Maechler wrote:
>> "PD" == Peter Dalgaard <[EMAIL PROTECTED]>
>> on 02 Sep 2005 18:48:24 +0200 writes:
>
>PD> "Milton Lopez" <[EMAIL PROTECTED]> writes:
>
>>> I appreciate the update. We will consider using Linux,
>>> which leads me to one more qu
>
> In some machines I don't get the segmentation fault problem, but I don't get
> the
> message "Just a simple test" either (when using "cg" as the subroutine's
> name).
> I believe this is bug in R because if I change my C interface again to return
> a
> 0 instead of a R_NilValue, and then us
On Fri, 9 Sep 2005, Gabor Grothendieck wrote:
>
> I personally put NEWS, WISHLIST and THANKS files in the 'inst'
> directory of all my source packages. This has the effect of copying them to
> the
> top level of the built version so that they are accessible from R via:
>
I'm not sure that WISHLI
On Fri, 9 Sep 2005, Gabor Grothendieck wrote:
> How about if there were just a standard location and name such as inst/NEWS,
> inst/WISHLIST, inst/THANKS (which has the advantage that they are
> automatically
> made available in the built package under the current way packages are
> built)
The pr
>
> Standard location or a mechachanism like the one you describe are both
> similar amount of work (and not much at all), the HTML pages are
> generated by perl and I have the parsed DESCRIPTION file there, i.e.,
> using a fixed name or the value of the Changelog field is basically
> the same.
>
On Sat, 10 Sep 2005, Gabor Grothendieck wrote:
>
> And one more comment. The DESCRIPTION file does not record the
> location or existence of the various subdirectories such as R, man,
> exec, etc. If NEWS is to be recorded as a meta data line item in
> DESCRIPTION then surely all of these should
On Sat, 10 Sep 2005, Frank E Harrell Jr wrote:
> I would vote for allowing a URL or external file name in in DESCRIPTION,
> whose contents could be automatically displayed for the user when
> needed. Our changelogs are automatically generated by CVS and are on
> the web.
Yes, this would be nice.
On Sat, 10 Sep 2005, Seth Falcon wrote:
> For what its worth, I don't like this idea of adding a ChangeLog field
> to the DESCRIPTION file.
>
> Agreeing upon a standard location for NEWS or CHANGES or some such
> seems a more simple solution. As long as the presence of such a file
> is *optional*.
On Sat, 10 Sep 2005, Gabor Grothendieck wrote:
> On 9/10/05, Thomas Lumley <[EMAIL PROTECTED]> wrote:
>> On Sat, 10 Sep 2005, Gabor Grothendieck wrote:
>>>
>>> And one more comment. The DESCRIPTION file does not record the
>>> location or existence of
On Fri, 16 Sep 2005, [EMAIL PROTECTED] wrote:
The name of the "continental" quotation mark « is "guillemet".
For anyone who is still confused:
Left pointing guillemet (U+00BB)
http://www.mathmlcentral.com/characters/glyphs/LeftGuillemet.html
Left pointing guillemot (Uria aalge)
http://www.r
On Fri, 16 Sep 2005, Thomas Lumley wrote:
On Fri, 16 Sep 2005, [EMAIL PROTECTED] wrote:
The name of the "continental" quotation mark ? is "guillemet".
For anyone who is still confused:
It should perhaps be noted that the Postscript name for the Unicode "Lef
27918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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nt(p[[i]])
# error 3: list subsripting with "" fails in second element
for (i in names(p))
print(p[i])
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On Mon, 3 Oct 2005, Duncan Murdoch wrote:
> On 10/3/2005 3:25 AM, Andrew Piskorski wrote:
>> R folks, I'm curious about possible support for Lisp-style macros in
>> R. I'm aware of the "defmacro" support for S-Plus and R discussed
>> here:
>>
>> http://www.biostat.wustl.edu/archives/html/s-news
e
> search terms which I used before :-(
>
>
> with regards
> Knut
>
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On Tue, 11 Oct 2005, Knut Krueger wrote:
>
> I found a definition of the SPSS files.
> http://www.wotsit.org/download.asp?f=spssdata
> but they recommend to use the spss input/output dll to ensure upward
> compatbility
>
"Well, they would say that, wouldn't they" (Rice-Davis 1963)
Unfortunately,
On Wed, 12 Oct 2005, Knut Krueger wrote:
> Thomas Lumley schrieb:
>> On Tue, 11 Oct 2005, Knut Krueger wrote:
>>> I found a definition of the SPSS files.
>>> http://www.wotsit.org/download.asp?f=spssdata
>>> but they recommend to use the spss input/output d
On Tue, 18 Oct 2005, Earl F. Glynn wrote:
> Whis is there a .Machine$sizeof.longdouble but no .Machine$sizeof.double?
>
sizeof(double) is always 8 and sizeof(int) is always 4, because R requires
the IEEE/IEC standard arithmetic types. R will not compile with any other
sizes.
-thomas
On Tue, 18 Oct 2005, Earl F. Glynn wrote:
> "Thomas Lumley" <[EMAIL PROTECTED]> wrote in message
> news:[EMAIL PROTECTED]
>> On Tue, 18 Oct 2005, Earl F. Glynn wrote:
>>
>>> Whis is there a .Machine$sizeof.longdouble but no
> .Machine$sizeof.double?
&
>>>
>>>> f <- function(x, y, p=1) {cat("in f\n"); (x*y)^p}
>>>> outer2(1:2, 3:5, f, 2)
>>>
>>> in f
>>> [,1] [,2] [,3]
>>> [1,]9 16 25
>>> [2,] 36 64 100
>>>
>>>> ou
On Mon, 31 Oct 2005, Liaw, Andy wrote:
>> From: Thomas Lumley
>>
>> On Sun, 30 Oct 2005, Jonathan Rougier wrote:
>>
>>> I'm not sure about this. Perhaps I am a dinosaur, but my feeling is
>>> that if people are writing functions in R that might
On Tue, 1 Nov 2005, Duncan Murdoch wrote:
> The version I posted yesterday did indeed mess up when some arguments were
> unspecified. Here's a revision that seems to work in all the tests I can
> think of. I also added the SIMPLIFY and USE.NAMES args from mapply to it,
> and a sanity check to
On Fri, 18 Nov 2005, Byron Ellis wrote:
> So, consider the following:
>
> > example(glm)
> > g = function(model) { w = runif(9);glm(model,weights=w); }
> > g(counts ~ outcome + treatment)
> Error in eval(expr, envir, enclos) : object "w" not found
>
> Huh?! I suspect that somebody is lazily evalua
>
> Using the biased variance just because it is the MLE (if that is the
> argument) seems confused to me. However, there's another point:
>
>> var(sample(1:3, 10, replace=TRUE))
> [1] 0.6680556
>
> i.e. if we are considering x as the entire population, then the
> variance when sampling from it
On Wed, 14 Dec 2005, Tony Plate wrote:
>
> That's what I was trying to say: the whole truth is that numeric index
> vectors that contain positive integral quantities can also contain
> zeros. Upon rereading this passage yet again, I think it is more
> misleading than merely incomplete: the phrasin
else sum((abs(x - E) - 0.5)^2/E)
> METHOD <- paste(METHOD, "with Yates' continuity correction")
> }
> else STATISTIC <- sum((abs(x - E))^2/E)
> ## replace end
>
mented and has been in S for a long
time.
-thomas
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On Mon, 9 Jan 2006, Martin Morgan wrote:
> I guess I have to say yes, I'd exepct
>
> x <- 1:10
> sum(x[x>10]) ==> numeric(0)
>
> this would be reinforced by recongnizing that numeric(0) is not zero,
> but nothing. I guess the summation over an empty set is an empty set,
> rather than a set contain
2,3.5,-1.3,3.1,
>>>
>> 3.2,3.1,-0.1,0.2,0.15,-0.05,-0.1,0.2,0.1,-0.1)
>>
>> Program received signal SIGINT, Interrupt.
>> 0x9001f208 in select ()
>> (gdb) break calcStepgram
>> Breakpoint 1 at 0x10bb418: file Stepgram.c
On Tue, 10 Jan 2006, Sean Davis wrote:
> and such. However, the call to the function is via .C; parameters from the
> .C call are not being passed correctly to the function. As an example, I
> have attached a GDB run of the code. I set a breakpoint on entry to the
> function I am calling from R.
On Tue, 10 Jan 2006, Sean Davis wrote:
>
> Thanks, Thomas. That did fix the initialization issue (or apparent one).
> Unfortunately, the reason that I started debugging was for segmentation
> faults, which have not gone away. However, it now looks like the problem is
> internal to the C++ code a
Since someone is bound to point this out soon I will note that
a) A discussion draft of the proposed GPL version 3 is up at
http://gplv3.fsf.org/
b) If you have comments on the draft, send them to the FSF rather than to
r-devel
-thomas
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On Mon, 23 Jan 2006, Hin-Tak Leung wrote:
> Prof Brian Ripley wrote:
>> We know: we even document it in the appropriate places.
>
> I went and have a look - it is the last section of R-admin (and of
> course, for those who "read the source", R/include/Rinternals.h). It
> would be good to mention t
On Mon, 23 Jan 2006, Hin-Tak Leung wrote:
>
> The 32-bit/64-bit issue affects purchasing or upgrading decisions
> - whether one wants to spend the money on buying cheaper
> 32-bit machines, versus more expensive 64-bit machines. That
> decision would be based on information available while *not* ha
Call
forcing lengths and integers to be passed as 32-bit. This would mean that the
code couldn't use large integers or large vectors, but it would keep working
indefinitely.
-thomas
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> Modified applydefine to duplicate if necessary to ensure that the
> assignment target in calls to assignment functions via the complex
> assignment mechanism always has NAMED == 1.
>
Yes, that was the one. It was reported as a bug back then too, and
there was quite a bit of di
in the dependency
tree.
-thomas
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will give the same answer a year later if I keep the old
versions. This isn't so much because of changes in R as because of
changes in packages.
-thomas
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think the five numbers come from four memory allocations before
example() is called. Looking at the code in src/main/memory.c, it
prints newline only when the call stack is not empty.
I don't see why this is done, and I may well be the person who did it
(I don't have svn on this computer to check), but it is clearly
deliberate.
-thomas
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e, and so clearly
deliberate not to, that I suspect there may have been a good reason.
If I can't work it out (after my grant deadline this week) I will just
assume it's wrong.
-thomas
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need not be a model frame in the fitted object. (it's optional)
2) More importantly, if you have y~sin(x), the model frame will
contain sin(x), not x. For what termplot() does, it has to be able to
reconstruct 'x', which isn't possible without the original data.
It's q
u are telling the
compiler you're passing ints to Rprintf(), but you are actually
passing doubles.
When I fix these problems the code works for me.
-thomas
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atural to retry
until the requested data are available?
-thomas
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ons that way, you need to make potentially
unsafe assumptions. For example, that you can't get an error halfway up a
chain of nested complex assignments when it's too late to back out of the
expression.
-thomas
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University of Auckland
y instead.
>
As a follow-up to this, note that with traditional Unix symbol
resolution it was forbidden to have two different routines with the
same name linked into an object. That just isn't an option for R
because of the package system. This isn't theoretical: the PACKAG
rsity of Sydney
> Camperdown NSW 2050
> Australia
Dario,
When you use the constructor, the environment of the function is the
environment inside the constructor; when you use new() it is
R_GlobalEnv
The way functions print is that they print their environment when it
isn't
in simple cases but
is hard to avoid in full generality.
-thomas
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atistics unit
> IRB Barcelona
> Tel (+34) 93 402 0553
> Fax (+34) 93 402 0257
>
> evarist.pla...@irbbarcelona.org
> http://www.irbbarcelona.org/bioinformatics
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r
general it's not
clear what (if anything) it means to have the same contrasts on
factors with different numbers of levels.
-thomas
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If .Call and .C re-enabled the GC on return from compiled code (and
threw some sort of error) that would help contain the potential
damage.
You'd might also want to re-enable GC if malloc() returned NULL,
rather than giving an out-of-memory error.
-thomas
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appened independently in R. I ported the 'survival'
version of rowsum() to R, added it to base R in version 0.63.1, and
later it made it faster using hashing.
So perhaps it isn't entirely StatSci's fault, although it's likely
that R would eventually have added a rowsum(
?
>
tracemem() isn't likely to give false positives. Since you're on
Linux, you could check by running under gdb and setting a breakpoint
on memtrace_report, which is the function that prints the message.
That would show where the duplicates are happening.
- thomas
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and lose
data, I would prefer to make the user decide what to do.
-thomas
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inputs into numbers
that are indistinguishable from uniform random except that the same
input always gives the same output.
What's harder is to prove that you *have* a good quality hash
function, but for these (non-adversarial) purposes even something like
MD4 would be fine, and certainly the SHA family.
-thomas
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because the use is guarded
by an if(), but CMD check can't tell this. So, it's a good idea to
remove all Notes that can be removed without introducing other code
problems, which is nearly all of them, but occasionally there may be a
good reason for code that produces a Note.
But if you
th a bound on the degree of freedom difference, but my copy
of Claeskens & Hjort's book on model selection and model averaging is
currently with a student so I can't be definitive.
-thomas
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___
orced to do that, but I thought it was supposed to be a last resort and
> that I was *supposed* to be able to fix my problems by proper use of
> imports.
'Imports' won't be enough -- the whole point of a generic is that it's
visible to the user, which doesn't happen with imports.
-thomas
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es on CRAN or
Bioconductor using it, and I can't think of any situation where it
would be used deliberately.
-thomas
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isn't a ... formal argument in
scope.
-thomas
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re should be
a warning, such as gcc's "control reaches end of a non-void function"
Also .C() doesn't pass SEXPs, so the declaration of the function is still
wrong for .C(), though this one the compiler won't notice.
--thomas
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P
an unfamiliar package.
-thomas
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est of
> leaving them in, however, clearly shows that it does no harm.
>
> Terry T.
>
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&
ty of the matrices are actually invertible.
You can probably do slightly better by replacing the chol2inv() with
backsolve(): solving just the systems of linear equations you need is
usually preferable to constructing a matrix inverse.
Note that this approach will give wrong answers without warnin
that it appears to be unavailable.
Any suggestions for how to fix this? I've tried uploading a new version of
RMonetDB, but the situation didn't change: it built successfully, but the
Linux check of sqlsurvey still couldn't find it.
-thomas
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object is out of scope" it seems harmless to be able to prevent finalizers
from running during a particular code block, but I can't see any way to do
it.
Suggestions?
-thomas
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[[alternative
m pretty sure we don't have a mechanism for temporarily suspending
> running the finalizers but it is probably fairly easy to add if that
> is the only option.
>
> I might be able to think of other options with more details on the
> issue.
>
> Best,
>
> luke
>
asible on
commodity desktops and laptops, and even on computers with enough memory,
the database (MonetDB) is faster.
-thomas
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ith analysis in memory even
if you ignore the data loading time.
For example, using a data set already in memory, with 18000 records and 96
variables:
> system.time(svymean(~BPXSAR+BPXDAR,subset(dhanes,RIAGENDR==2)))
user system elapsed
0.090.010.10
Using MonetDB
...)
but it seems that could have different lazy-evaluation behaviour.
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he log(n) term is kept and various terms of
order 1 are discarded. What we're arguing about is one of the O(1) terms.
If it makes an important difference then presumably we should also worry
about the other O(1) terms that got discarded.
-thomas
--
Thomas Lumley
Professor of Biost
.)
>
>
> Is there any workaround or do I have to rename the t.test.speclib function
> to
> something like t_test.speclib?
>
> Thank you in advance
>
> Lukas
> [[alternative HTML version deleted]]
>
> ______
> R-
mmers were better able to cope and that dropping dimensions was
preferable.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUniversity of Washington, Seattle
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istinfo/r-devel
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macbook 2.16ghz)
That's not where the cost would be. PROTECT/UNPROTECT calls themselves are
very cheap, since they just push and pop pointers from a stack. Any real impact
of different strategies in using PROTECT would be seen in the garbage
collector.
-thomas
Thomas Lumley
I ended up creating a new odfWeave.survey package that depends on
odfWeave and survey, but this seems like the sort of thing that should be able
to be done with Enhances or Suggests.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
t.org/doc/manuals/R-exts.html#Package-structure
[4] http://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file
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-thomas
Thomas Lumley
the software
infrastructure from the Bioconductor project.
The instructors will be Thomas Lumley and Ken Rice.
Further details on this and the other 21 modules at the Summer Institute are
available from http://sisg.biostat.washington.edu/. I will just note that this
is the University of
tual source directory. Is there any way around that?
Not really. You could always manage your files in a separate directory tree
and then use a Makefile to put them into the package format.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.edu
levels.
For example:
A <- factor("orange",levels=c("orange","yellow","red","purple"))
B <- factor("orange", levels=c("orange","apple","mango", "banananana"))
On the other hand, I think the curre
required.
NA is different, because NA by its nature can't compare equal to anything: x==NA asks: "Is x
equal to some number I don't know?", to which the answer is "Don't know".
x==Inf asks "Is x positive infinite?", which is a perfectly well-defined
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