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
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
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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atural to retry
until the requested data are available?
-thomas
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.)
>
>
> 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-
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
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Professor of Biost
...)
but it seems that could have different lazy-evaluation behaviour.
-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
asible on
commodity desktops and laptops, and even on computers with enough memory,
the database (MonetDB) is faster.
-thomas
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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
>
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
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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Professor of Biosta
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
est of
> leaving them in, however, clearly shows that it does no harm.
>
> Terry T.
>
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&
an unfamiliar package.
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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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isn't a ... formal argument in
scope.
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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.
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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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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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___
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
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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and lose
data, I would prefer to make the user decide what to do.
-thomas
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?
>
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
--
Thomas Luml
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(
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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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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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
in simple cases but
is hard to avoid in full generality.
-thomas
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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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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
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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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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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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in the dependency
tree.
-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
f you are not the intended recipient of the e-mail you may not
use, disclose, copy, redirect or print the content. If this e-mail is not
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###
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R-
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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other 'dangerous' functions I need to intercept (
".Internal" perhaps ?)
All comments and suggestions are welcomed,
thanks,
-gordon
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T
erstand what worrisome sign it tries to speak of.
-thomas
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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
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
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
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
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
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
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
istinfo/r-devel
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: jas...@bu.edu
PyMOLWiki : http://www.pymolwiki.org/
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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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users probably don't have /dev/random
-thomas
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fied
It works for me. I suspect it's a permission problem or something similar
on your system.
Duncan Murdoch
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additional minor issues with the documentation which were raised in a
separate thread.
Regards,
vQ
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ong-format variable names are x and y and the conditions to be put in the
time variable are Before and After.
-thomas
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since reported, the 'missing values are
ignored' statement in ?quantile is wrong (or at least incomplete).
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUniversity of Washington, Seattle
_
quot;bigglm", signature=c("formula","data"))
bigglm.data.frame<-function(formula, data, ..., chunksize=5000){
setMethod("bigglm",
c("ANY","DBIConnection"),
function(formula, data, family = gaussian(),
will be ignored
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S3 inheritance on SQLiteConnection (which works, but doesn't
extend to other DBIConnection objects, as you pointed out previously).
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUniversity of Washington, Seattle
function; S3 methods will not likely be found
2: In methods("bigglm") : function 'bigglm' appears not to be generic
[This is R 2.7.2, admittedly a little ancient]
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.edu
ge sent from CompuServe - visit us today at http://www.cs.com
Email message sent from CompuServe - visit us today at http://www.cs.com
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ist
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idn't really
eventuate.
-thomas
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alue = 13:15)
which is somewhat confusing, because then '*tmp*' appears in the trace
somewhat ex machina. (again, the explanation is in the source code, but
the traceback could have been more informative.)
cheers,
vQ
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works may just be an
inconsistency -- as you can see from previous discussions, R often does not
effectively forbid code that shouldn't work -- or it may be bug-compatibility
with some version of S or S-PLUS.
-thomas
Thomas Lumley Assoc. Professor, Biostatistic
n
the evaluation order of the *apply family (eg, does apply process the columns
left to right, or right to left, or however it feels like?).
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUni
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some version
of the GPL or LGPL?
Also, according to the FSF, the CPL used in Ipopt is technically incompatible
with the GPL because of its choice of law clause.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUniversity of Washington
he CPU usage to 100%, but
the success of ATLAS suggests that they may really be limited more by cpu
memory bandwidth. I don't know if this counts.
Other people may have different suggestions.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.
ndard palette isn't ideal, though.
-thomas
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ed some way to make the implementation
easier (money, code, new approaches to the programming,...).
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUniversity of Washington, Seattle
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,]
not work
This is also not a bug. The drop= option to [ controls what happens when the
subset has dimensions of length 1. If you want subset to be a data frame in
this context, use
subset <- data.frame[,'x',drop=FALSE]
and then subset[&#
CE exports.
I'm almost certainly missing something obvious - please point it out.
Based on the r-forge code it looks like you need library(survival) in R code in
tests/. It doesn't happen automatically like it does for examples.
-thomas
Thomas Lumley Assoc
use) Linux, then valgrind is an excellent tool
for this. There's some documentation in 'Writing R Extensions'. Valgrind
runs your code in a virtual machine and tracks all memory accesses, so it
often will even find bugs in C code that are hard to reproduce.
balEnv, package:stats, package:graphics, package:grDevices, package:utils,
package:datasets, package:methods, Autoloads, package:base
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Thomas Lumley Assoc. Pro
On further research it looks as though this has already been fixed (though it
wasn't mentioned in NEWS, so it wasn't immediately obvious).
You could try the patched build from http://r.research.att.com/
-thomas
Thomas Lumley Assoc. Professor, Biostatist
like antialiasing.
The gap doesn't appear in pdf().
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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mputer truncation error.
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_
e
> same result as assigning any other object. So I was surprised when
> assigning a NULL in fact removed the element from the list. Is this an
> intended behaviour?
Yes.
> If so, does anybody know where is it documented and
> what is a good way around?
>
One place is FAQ 7.
fairly realistic about the
lack of difference between 4e-16 and 5e-16.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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h
r-help or r-devel that produces behaviour they
don't understand and asks if it is bug (rather than asserting that it must be a
bug) they have a much higher chance of receiving a friendly reply [and an even
higher chance of receiving a helpful reply]
-thomas
Thomas Luml
) and on Linux(64bit R).
-thomas
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ng seems ok
>> lmtest<-lm(y~x1+x2)
>> summary(lmtest)$r.sq
> [1] 0.9342672
>> 1-sum(lmtest$res^2)/sum((y-mean(y))^2)
> [1] 0.9342672
>
> __
> R-devel@r-project.org mailing list
>
numero di
colonne
--> change "elemtni" to "elementi"
Regards
Luca
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Thomas Lumley Assoc. Professor, Biostatistics
[EMA
nt is easy.
Other advice about larger or smaller SQLite cache size didn't seem to have much
impact in my setting, and I didn't try the advice about getting a different
database.
Despite it's many other virtues, SQLite is still slow at indexing.
Thanks to all.
-thomas
On Mon, 22 Oct 2007, hadley wickham wrote:
> On 10/22/07, Thomas Lumley <[EMAIL PROTECTED]> wrote:
>>
>> I am trying to use RSQLite for storing data and I need to create indexes on
>> two variables in the table. It appears from searching the web that the CREATE
>
oping
there is some simple solution.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
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On Wed, 10 Oct 2007, Duncan Murdoch wrote:>
> As Charles Berry told you when this was posted to R-help, it looks as
> though it is Mathematica that is inaccurate. For example, I would
> expect this plot to be smooth, and it is not in either R or Mathematica,
> but R is at least monotone:
I did ch
On Wed, 10 Oct 2007, [EMAIL PROTECTED] wrote:
> Full_Name: Martin Schlather
> Version: R version 2.7.0 Under development (unstable) (2007-10-01 r43043)
> OS: Linux
> Submission from: (NULL) (91.3.209.203)
>
>
> Hi,
>
> There are 2 dangers with using 'DUP=FALSE' mentioned:
> * formal arguments
>
On Mon, 6 Aug 2007, Petr Savicky wrote:
> Question.
>
> Is there a way how to optimize a function written in C
> using optim?
The algorithms used by optim are all accessible from C. The manual
"Writing R Extensions" has a section on "The R API", including the
optimization routines.
-th
On Wed, 27 Jun 2007, Ben Bolker wrote:
>
> I did some trawling on the ISI web of science,
> selecting all papers citing all papers
> with "R DEV COR TEAM" in the author field
> (which is how ISI seems to be tagging things).
It's not quite that simple. If people use the recommended citation then
n applied to an empty vector, gives the
identity element for the operator. The identity element for AND is TRUE.
>
> Does this make any sense?
>
Yes, although it is initially surprising.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED]
On Fri, 25 May 2007, Sean Davis wrote:
> On Friday 25 May 2007 05:02, Gatsu wrote:
>> Can somebody help me?
>>
>> I need the C/C++ code for the R's qbeta function.
>
> R is open-source, so you can simply download the source and look at whatever
> parts you like.
>
Finding the qbeta function may t
ing with it, but ... this is the first time I ever touch
>> a Perl script.
>>
>>
>> Cheers,
>>
>> Romain
>>
>>
>>
>>
>>> version
>>>
>>
>> _
>> platform
>> i686-pc-linux-gnu
>> arch
>> i686
>> os
>> linux-gnu
>> system i686,
>> linux-gnu
>> status Under development
>> (unstable)
>> major
>> 2
>> minor 6.0
>> year
>> 2007
>> month
>> 03
>> day
>> 30
>> svn rev
>> 40983
>> language
>> R
>> version.string R version 2.6.0 Under development (unstable) (2007-03-30
>> r40983)
>>
> --
> Mango Solutions
> data analysis that delivers
>
> Tel: +44(0) 1249 467 467
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>
>
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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On Fri, 16 Mar 2007, Martin Morgan wrote:
> Is there a (C or R) function to invalidate the relevant parts of SEXP
> / data that are inaccessible? My problem is in tracking down
> protection and other memory mismanagement bugs, where I have to rely
> on luck to invalidate or overwrite data to trigg
work. Those are the ones that are documented.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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ous problem
>
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Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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vel@r-project.org mailing list
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Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle__
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al to use R_alloc et al because C++ allocation/
>> deallocation involves constructors/destructors and because the C++
>> code is also compiled into a standalone binary (I would rather avoid
>> maintaining two separate versions).
>>
>> ______
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