Cole,
Bioconductor's high throughput sequencing infrastructure package IRanges
contains code that may be useful for speeding up base::rbind.data.frame.
I've extracted the salient bits from that rbind method, but left the
corner case handling code out. IRanges's rbind method took the approach
of
This issue ties loosely into other recent S4 topics on this board.
The methods package defines a number of implicit generics for linear
algebra related functions (rcond, norm, backsolve) that, when used,
interfere with base package operations. Here is the cut-and-paste
version of the code the
,
Patrick
On Feb 16, 2012, at 5:08 PM, Patrick Aboyoun wrote:
> I stumbled across one of those intermittent bugs where the code sometimes
> works and sometimes doesn't. Below is an example run showing a failure where
> a CHARSXP object was not properly created (by the sub function
I stumbled across one of those intermittent bugs where the code
sometimes works and sometimes doesn't. Below is an example run showing
a failure where a CHARSXP object was not properly created (by the sub
function?). I was able to reproduce this error on three different R
builds in fresh R ses
I was having a hard time finding the all.vars function (and wound up
creating a poor man's version -- see below). I see that there are links to
all.vars in the stats/man/case.names.Rd and stats/man/formula.Rd. I was
wondering if more crosslinks could be made for this function, particularly
in base/
I've stumbled across an issue with aggregate.ts that either is due to a
misuse of %/% or something deeper relating to numerical precision on
Windows. The test code is
x <- rep(6:10, 1:5)
as.vector(aggregate(as.ts(x), FUN = mean, ndeltat = 5))
On Linux and Mac I get the correct answer
> x <- r
Forgive the multiple posts, but I am resending a issue under a new
subject so it doesn't get lost. There is inconsistent behavior between
is and extends for class ANY. All classes (even non-existent ones)
extend ANY according to methods::extends, but only S4 objects are of
class ANY according t
atrick
Simon Urbanek wrote:
On Sep 8, 2009, at 12:39 , Simon Urbanek wrote:
On Sep 8, 2009, at 12:14 , Patrick Aboyoun wrote:
This is a reissue of a question I had asked a few weeks ago to see
if anyone had any thoughts on the matter.
I am looking to have slot in an S4 class definition
This is a reissue of a question I had asked a few weeks ago to see if
anyone had any thoughts on the matter.
I am looking to have slot in an S4 class definition that can take any
(S3 or S4) object. The ANY class seemed to be a good candidate, but the
is() function definition performs an S3Case
I am looking to have slot in an S4 class definition that can take any
(S3 or S4) object. The ANY class seemed to be a good candidate, but the
is() function definition performs an S3Case test before checking if
methods:::.identC(class2, "ANY"). The result is the is() function does
not consider v
I have been retooling an S4 class definition to include another slot and
have found that the methods::validObject function (defined in
methods/R/SClasses.R) in R-devel throws an error that isn't caught
internally (and thus not controllable by 'test' argument) when
retrieving a non-existent slot
Saptarshi,
I know of two alternatives you can use to do fast extraction of
consecutive subsequences of a vector:
1) Fast copy: The method you mentioned of creating a memcpy'd vector
2) Pointer management: Creating an externalptr object in R and manage
the start and end of your data
If you
Thanks Brian. I'll stop trying to hack the code to work and opt for the
dll rename option.
Patrick
Prof Brian Ripley wrote:
On Fri, 24 Apr 2009, Patrick Aboyoun wrote:
I am having a problem using two DLLs with the same name, but
obviously located in different directories, in an R se
I am having a problem using two DLLs with the same name, but obviously
located in different directories, in an R session. The troublesome
package is the (Bioconductor) Rgraphviz package. It relies on (3rd party
software) graphviz and imports functions from (Bioconductor) package
graph. Unfortun
you move it to a different
> machine, where the full path to Sweave.sty is different.
>
> Duncan Murdoch
>
>>
>>
>> Cheers,
>> Patrick
>>
>>
>> Duncan Murdoch wrote:
>>> On 09/04/2008 5:23 PM, Patrick Aboyoun wrote:
>>>> So
doch wrote:
> On 09/04/2008 5:23 PM, Patrick Aboyoun wrote:
>> Something funky happened to my e-mail. I was trying to paste
>> information related to MiKTeX and R into my message and it appears to
>> have corrupted the text somehow. Anyway, the message I was trying to
>
Something funky happened to my e-mail. I was trying to paste information
related to MiKTeX and R into my message and it appears to have corrupted
the text somehow. Anyway, the message I was trying to get across is that
the tex file contains the path
\usepackage{E:/paboyoun/BBS-2~1.2-B/R/share/
In the process of updating R to R 2.7 alpha or R 2.7 beta for the
BioConductor 2.2 builds on Windows, I have hit a snag because the BioC
build system has long path names (e.g. D:\biocbld\bbs-2.2-bioc\R) and
these path names are not resolving properly by MiKTeX 2.7 during
vignette construction.
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