Re: [Bioc-devel] SummarizedExperiment initialisation and manipulation question.
Thanks for the quick action :-) Nico --- Nicolas Delhomme, PhD The Street Lab Department of Plant Physiology Umeå Plant Science Center Tel: +46 90 786 5478 Email: nicolas.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --- On 30 Jun 2015, at 07:56, Hervé Pagès hpa...@fredhutch.org wrote: Done in SummarizedExperiment 0.3.2. Thanks for the feedback, H. On 06/29/2015 10:26 PM, Hervé Pagès wrote: Hi Nico, It seems reasonable indeed to support rowRanges- on SummarizedExperiment0. It might be a little bit surprising for the user that the setter changes the class of the object but it looks like a perfectly legit situation for doing so here. Also there are some precedents: x - 1:5 x[1] - a x [1] a 2 3 4 5 and: library(Biostrings) dna - DNAString(GGATTAAA) class(dna) # DNAString masks(dna) - Mask(length(dna), 2, 5) class(dna) # MaskedDNAString I'll add this, unless someone has a better idea? Thanks, H. On 06/29/2015 03:13 AM, Nicolas Delhomme wrote: Hej alla! In the simpleRNASeq function of the easyRNASeq package, I start by instantiating a SummarizedExperiment object not initially providing the rowRanges. This results in the creation of an object of the class SummarizedExperiment0. When later, once I have validated the annotation, I try to extend the rowRanges of my SummarizedExperiment object, I get an error message that rowRanges- is not implemented for signature SummarizedExperiment0, GRangesList. I'm now wondering if this has been omitted on purpose for SummarizedExperiment0 objects or is not yet implemented. The reason I'm wondering is because there is the possibility to cast a SummarizedExperiment0 object as a RangedSummarizedExperiment (which is my current work-around), but I'm wondering if that's the best way to go. I don't have access to my Rsession right now, so no sessionInfo(), but I'm using R3.2.1 on OSX 10.10.3 (Yosemite), and the latest devel packages (updated today; SummarizedExperiment version is 0.3.0). Cheers, Nico --- Nicolas Delhomme, PhD The Street Lab Department of Plant Physiology Umeå Plant Science Center Tel: +46 90 786 5478 Email: nicolas.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --- ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Rd] additional leap second
hi, Index: leap_second/src/library/base/R/zdatetime.R === --- leap_second/src/library/base/R/zdatetime.R(revision 68608) +++ leap_second/src/library/base/R/zdatetime.R(working copy) @@ -24,7 +24,8 @@ 1979-12-31, 1981-6-30, 1982-6-30, 1983-6-30, 1985-6-30, 1987-12-31, 1989-12-31, 1990-12-31, 1992-6-30, 1993-6-30, 1994-6-30,1995-12-31, - 1997-6-30, 1998-12-31, 2005-12-31, 2008-12-31, 2012-6-30) + 1997-6-30, 1998-12-31, 2005-12-31, 2008-12-31, + 2012-6-30, 2015-6-30) .leap.seconds - strptime(paste(.leap.seconds , 23:59:60), %Y-%m-%d %H:%M:%S) c(as.POSIXct(.leap.seconds, GMT)) # lose the timezone Best Regards, -- Eiji NAKAMA nakama (a) ki.rim.or.jp \u4e2d\u9593\u6804\u6cbb nakama (a) ki.rim.or.jp __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] additional leap second
On 01/07/2015 7:20 AM, Ei-ji Nakama wrote: hi, Index: leap_second/src/library/base/R/zdatetime.R === --- leap_second/src/library/base/R/zdatetime.R(revision 68608) +++ leap_second/src/library/base/R/zdatetime.R(working copy) @@ -24,7 +24,8 @@ 1979-12-31, 1981-6-30, 1982-6-30, 1983-6-30, 1985-6-30, 1987-12-31, 1989-12-31, 1990-12-31, 1992-6-30, 1993-6-30, 1994-6-30,1995-12-31, - 1997-6-30, 1998-12-31, 2005-12-31, 2008-12-31, 2012-6-30) + 1997-6-30, 1998-12-31, 2005-12-31, 2008-12-31, + 2012-6-30, 2015-6-30) .leap.seconds - strptime(paste(.leap.seconds , 23:59:60), %Y-%m-%d %H:%M:%S) c(as.POSIXct(.leap.seconds, GMT)) # lose the timezone Best Regards, -- Eiji NAKAMA nakama (a) ki.rim.or.jp \u4e2d\u9593\u6804\u6cbb nakama (a) ki.rim.or.jp Thanks, I'll add it to R-devel and R-patched. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?
A slightly simpler formulation of the problem is:
show - function(...) stop(My show!)
methods::setClass(Person, slots = list(name = character))
methods::new(Person, name = Tom)
# Error in (function (...) : My show!
Hadley
On Tue, Jun 30, 2015 at 9:02 AM, Dean Attali daatt...@gmail.com wrote:
Hi r-devel
If you define a function named `show` or attach a package with an exported
`show` function, then printing/vieweing S4 objects breaks. This is probably
because the `print` function calls `show`, which is now masked.
Example:
show - function() {}
setClass(Person, slots = list(name = character))
tom - new(Person, name = Tom)
tom # error
methods::show(tom) # works
The error was a surprise to me because I was under the assumption that
`show` would be namespaced and therefore should not break.
I'm wondering if this is intended behaviour, or if this is a problem. My
intuition, and Hadley agreed on Twitter, is that defining a `show` method
should not have such a grave effect on printing S4 objects.
Thanks
---
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Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?
On 30/06/2015 1:57 PM, Hadley Wickham wrote:
A slightly simpler formulation of the problem is:
show - function(...) stop(My show!)
methods::setClass(Person, slots = list(name = character))
methods::new(Person, name = Tom)
# Error in (function (...) : My show!
Just to be clear: the complaint is that the auto-called show() is not
methods::show? I.e. after
x - methods::new(Person, name = Tom)
you would expect
show(x)
to give the error, but not
x
??
Duncan Murdoch
Hadley
On Tue, Jun 30, 2015 at 9:02 AM, Dean Attali daatt...@gmail.com wrote:
Hi r-devel
If you define a function named `show` or attach a package with an exported
`show` function, then printing/vieweing S4 objects breaks. This is probably
because the `print` function calls `show`, which is now masked.
Example:
show - function() {}
setClass(Person, slots = list(name = character))
tom - new(Person, name = Tom)
tom # error
methods::show(tom) # works
The error was a surprise to me because I was under the assumption that
`show` would be namespaced and therefore should not break.
I'm wondering if this is intended behaviour, or if this is a problem. My
intuition, and Hadley agreed on Twitter, is that defining a `show` method
should not have such a grave effect on printing S4 objects.
Thanks
---
http://deanattali.com
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Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?
On Tue, Jun 30, 2015 at 2:20 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 30/06/2015 1:57 PM, Hadley Wickham wrote: A slightly simpler formulation of the problem is: show - function(...) stop(My show!) methods::setClass(Person, slots = list(name = character)) methods::new(Person, name = Tom) # Error in (function (...) : My show! Just to be clear: the complaint is that the auto-called show() is not methods::show? I.e. after x - methods::new(Person, name = Tom) you would expect show(x) to give the error, but not x ?? Correct - I'd expect print() to always call methods::show(), not whatever show() is first on the search path. Hadley -- http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?
On 30/06/2015 5:27 PM, Lorenz, David wrote:
There is something I'm really missing here. The function show is a
standardGeneric function, so the correct way to write it as method like
this:
That describes methods::show. The problem is that the default print
mechanism isn't calling methods::show() (or base::print() as Luke says),
it's calling show() or print() in the global environment, so the user's
function overrides the generic, and you get the error.
Luke, are you going to look at this, or should I?
Duncan Murdoch
setMethod(show, Person, function(object) {
for an object of class Person for example.
Dave
On Tue, Jun 30, 2015 at 10:11 AM, luke-tier...@uiowa.edu wrote:
Same thing happens with S3 if you redefine print(). I thought that
code was actually calculating the function to call rather than the
symbol to use, but apparently not. Shouldn't be too hard to fix.
luke
On Tue, 30 Jun 2015, Hadley Wickham wrote:
On Tue, Jun 30, 2015 at 2:20 PM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
On 30/06/2015 1:57 PM, Hadley Wickham wrote:
A slightly simpler formulation of the problem is:
show - function(...) stop(My show!)
methods::setClass(Person, slots = list(name = character))
methods::new(Person, name = Tom)
# Error in (function (...) : My show!
Just to be clear: the complaint is that the auto-called show() is not
methods::show? I.e. after
x - methods::new(Person, name = Tom)
you would expect
show(x)
to give the error, but not
x
??
Correct - I'd expect print() to always call methods::show(), not
whatever show() is first on the search path.
Hadley
--
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Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics andFax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke-tier...@uiowa.edu
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Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?
There is something I'm really missing here. The function show is a
standardGeneric function, so the correct way to write it as method like
this:
setMethod(show, Person, function(object) {
for an object of class Person for example.
Dave
On Tue, Jun 30, 2015 at 10:11 AM, luke-tier...@uiowa.edu wrote:
Same thing happens with S3 if you redefine print(). I thought that
code was actually calculating the function to call rather than the
symbol to use, but apparently not. Shouldn't be too hard to fix.
luke
On Tue, 30 Jun 2015, Hadley Wickham wrote:
On Tue, Jun 30, 2015 at 2:20 PM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
On 30/06/2015 1:57 PM, Hadley Wickham wrote:
A slightly simpler formulation of the problem is:
show - function(...) stop(My show!)
methods::setClass(Person, slots = list(name = character))
methods::new(Person, name = Tom)
# Error in (function (...) : My show!
Just to be clear: the complaint is that the auto-called show() is not
methods::show? I.e. after
x - methods::new(Person, name = Tom)
you would expect
show(x)
to give the error, but not
x
??
Correct - I'd expect print() to always call methods::show(), not
whatever show() is first on the search path.
Hadley
--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics andFax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke-tier...@uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?
Same thing happens with S3 if you redefine print(). I thought that code was actually calculating the function to call rather than the symbol to use, but apparently not. Shouldn't be too hard to fix. luke On Tue, 30 Jun 2015, Hadley Wickham wrote: On Tue, Jun 30, 2015 at 2:20 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 30/06/2015 1:57 PM, Hadley Wickham wrote: A slightly simpler formulation of the problem is: show - function(...) stop(My show!) methods::setClass(Person, slots = list(name = character)) methods::new(Person, name = Tom) # Error in (function (...) : My show! Just to be clear: the complaint is that the auto-called show() is not methods::show? I.e. after x - methods::new(Person, name = Tom) you would expect show(x) to give the error, but not x ?? Correct - I'd expect print() to always call methods::show(), not whatever show() is first on the search path. Hadley -- Luke Tierney Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: luke-tier...@uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Why doesn't R have a float data type?
This is strictly a curiosity question. I am aware the R doesn't possess a float data type. I also don't mean to request that such functionality be implemented as I'm sure it would require a large amount of work with potential back compatibility conflicts. But I wanted to know why R has never had a float data type available? Regards, Charles [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Why doesn't R have a float data type?
Hi Greg, I was referring to the single precision type. Your points were what I expected. I just wanted to ask the R community if there was any other reason than 'there wasn't any reason to implement it'. Thanks, Charles On Tue, Jun 30, 2015 at 12:29 PM, Greg Snow 538...@gmail.com wrote: My understanding is that R does have a float type, it is just called double instead of float. If you are referring to a single precision floating point type, then R does have the as.single function, but that does not really change the way the number is stored, just sets a flag so that the proper conversion is done when passing to the .C or .fortran functions. The original S language and S+ would store things in single precision if needed, but for computations these values were almost always converted to doubles for precision. By the time R was developed the memory saving of using single precision instead of double precision was not as big an issue, so I expect that nobody ever considered it worth the effort to fully implement the single precision storage. If you mean something else other than the above by float data type then please give us more details so that we can better answer the question. On Tue, Jun 30, 2015 at 10:42 AM, Charles Determan cdeterma...@gmail.com wrote: This is strictly a curiosity question. I am aware the R doesn't possess a float data type. I also don't mean to request that such functionality be implemented as I'm sure it would require a large amount of work with potential back compatibility conflicts. But I wanted to know why R has never had a float data type available? Regards, Charles [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Bioc-devel] rtracklayer bug?
Hi Arne,
So this time when I look at the bioc-devel email list, I don't see a
record for this last name (or this email). In fact the only way I could
be sure it was you was that your post was the same... ;) If you want to
post from gmail, then you will need to subscribe the gmail address to
the list here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Marc
On 06/30/2015 02:26 AM, Arne Müller wrote:
Hello,
I think there’s a problem in UCSCSession initializer in rtracklayer:
setMethod(initialize, UCSCSession,
function(.Object, url =http://genome.ucsc.edu/cgi-bin/;,
user =ULL, session = NULL, force = FALSE, ...)
{
.Object@url - url
.Object@views - new.env()
gwURL - ucscURL(.Object, gateway)
if (force) {
gwURL - paste0(gwURL, '?redirect=anual')
}
gw - httpGet(gwURL, cookiefile =empfile(), header = TRUE,
.parseúLSE)
if (grepl(redirectTd, gw)) {
url - sub(.*?a href=h([^[:space:]]+cgi-bin/).*,
h\\1, gw)
return(initialize(.Object, url, user=er, session=session,
force=UE, ...))
}
cookie - grep(Set-[Cc]ookie: hguid[^==, gw)
if (!length(cookie))
stop(Failed to obtain 'hguid' cookie)
hguid - sub(.*Set-Cookie: (hguid[^==[^;]*);.*, \\1, gw)
.Object@hguid - hguid
if (!is.null(user) !is.null(session)) { ## bring in other
session
ucscGet(.Object, tracks,
list(hgS_doOtherUser =submit, hgS_otherUserName user,
hgS_otherUserSessionName =ession))
}
.Object
})
Shouldn’t ‘…’ be passed to httpGet that in turn is passed to RCURL, I.e.
gw - httpGet(gwURL, cookiefile =empfile(), header = TRUE,
.parseúLSE, …) ?
We run an internal instance of the UCSC genome browser and need to pass a
cookie to all http-requests. The problem is that
session =ew ('UCSCSession', url=myInternalURL, cookie=myAuthCookie)
Does not pass the ‘cookie’ argument to httpGet.
Regards,
Arne
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Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?
On 06/30/2015 11:33 AM, Duncan Murdoch wrote:
On 30/06/2015 5:27 PM, Lorenz, David wrote:
There is something I'm really missing here. The function show is a
standardGeneric function, so the correct way to write it as method like
this:
That describes methods::show. The problem is that the default print
mechanism isn't calling methods::show() (or base::print() as Luke says),
it's calling show() or print() in the global environment, so the user's
function overrides the generic, and you get the error.
These are two different problems aren't they? I can see that you might
want to ensure that base::print() calls methods::show(), but forcing the
default print to go to base::print(), rather than whatever print() is
first on the search path, would seem like a real change of philosophy.
What about all the other base functions that can be overridden by
something in the global environment?
Paul
Luke, are you going to look at this, or should I?
Duncan Murdoch
setMethod(show, Person, function(object) {
for an object of class Person for example.
Dave
On Tue, Jun 30, 2015 at 10:11 AM, luke-tier...@uiowa.edu wrote:
Same thing happens with S3 if you redefine print(). I thought that
code was actually calculating the function to call rather than the
symbol to use, but apparently not. Shouldn't be too hard to fix.
luke
On Tue, 30 Jun 2015, Hadley Wickham wrote:
On Tue, Jun 30, 2015 at 2:20 PM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
On 30/06/2015 1:57 PM, Hadley Wickham wrote:
A slightly simpler formulation of the problem is:
show - function(...) stop(My show!)
methods::setClass(Person, slots = list(name = character))
methods::new(Person, name = Tom)
# Error in (function (...) : My show!
Just to be clear: the complaint is that the auto-called show() is not
methods::show? I.e. after
x - methods::new(Person, name = Tom)
you would expect
show(x)
to give the error, but not
x
??
Correct - I'd expect print() to always call methods::show(), not
whatever show() is first on the search path.
Hadley
--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics andFax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke-tier...@uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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Re: [Rd] Why doesn't R have a float data type?
My understanding is that R does have a float type, it is just called double instead of float. If you are referring to a single precision floating point type, then R does have the as.single function, but that does not really change the way the number is stored, just sets a flag so that the proper conversion is done when passing to the .C or .fortran functions. The original S language and S+ would store things in single precision if needed, but for computations these values were almost always converted to doubles for precision. By the time R was developed the memory saving of using single precision instead of double precision was not as big an issue, so I expect that nobody ever considered it worth the effort to fully implement the single precision storage. If you mean something else other than the above by float data type then please give us more details so that we can better answer the question. On Tue, Jun 30, 2015 at 10:42 AM, Charles Determan cdeterma...@gmail.com wrote: This is strictly a curiosity question. I am aware the R doesn't possess a float data type. I also don't mean to request that such functionality be implemented as I'm sure it would require a large amount of work with potential back compatibility conflicts. But I wanted to know why R has never had a float data type available? Regards, Charles [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Why doesn't R have a float data type?
On 30/06/2015 17:42, Charles Determan wrote: This is strictly a curiosity question. I am aware the R doesn't possess a float data type. I also don't mean to request that such functionality be implemented as I'm sure it would require a large amount of work with potential back compatibility conflicts. But I wanted to know why R has never had a float data type available? You said it: 'it would require a large amount of work' and not just for R but also for many packages that users would expect to support data in that format. By the time R started to spread (late 90s), most FPUs were primarily double/extended precision and there was little or no speed advantage to single-precision calculations. And although S[-PLUS] had a 'single' type, we knew it was little used by then. For a few people the storage size may matter (and for others the 32-bit logicals are wasteful): although for most people RAM is cheap enough, there are packages such as 'ff' which address this. Regards, Charles -- Brian D. Ripley, rip...@stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford 1 South Parks Road, Oxford OX1 3TG, UK __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Why doesn't R have a float data type?
Hi Charles, Probably for the same reason it doesn't have short int, short unsigned int, long int, long unsigned int, long long int, long long unsigned int, long double etc... There are many built-in types in C and, in order to keep things simple, I guess the line had to be drew somewhere. Said otherwise, I don't think the atomic types in R were ever meant to reflect exactly what's available in C. Note that some CRAN packages (e.g. bit64) try to remedy this by providing support for atomic-like types that are not natively supported by R. I don't know if there is one for float though. Cheers, H. On 06/30/2015 09:42 AM, Charles Determan wrote: This is strictly a curiosity question. I am aware the R doesn't possess a float data type. I also don't mean to request that such functionality be implemented as I'm sure it would require a large amount of work with potential back compatibility conflicts. But I wanted to know why R has never had a float data type available? Regards, Charles [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?
On 30/06/2015 7:04 PM, Paul Gilbert wrote:
On 06/30/2015 11:33 AM, Duncan Murdoch wrote:
On 30/06/2015 5:27 PM, Lorenz, David wrote:
There is something I'm really missing here. The function show is a
standardGeneric function, so the correct way to write it as method like
this:
That describes methods::show. The problem is that the default print
mechanism isn't calling methods::show() (or base::print() as Luke says),
it's calling show() or print() in the global environment, so the user's
function overrides the generic, and you get the error.
These are two different problems aren't they? I can see that you might
want to ensure that base::print() calls methods::show(), but forcing the
default print to go to base::print(), rather than whatever print() is
first on the search path, would seem like a real change of philosophy.
What about all the other base functions that can be overridden by
something in the global environment?
I'd guess it's a minority of R users who know that print() or show() is
being called when you just evaluate an expression. Most would think R
just shows you the value of the expression. That's why they'd be
surprised when their local function suddenly stops the display of
variables from working.
On the other hand, if someone defined a print or show *method* in the
global environment, I think that one should override one defined in a
package namespace. It does now, and I wouldn't change that. The
difference is that I'd expect someone defining a method to know what
they're doing, but just defining a function doesn't imply that.
Duncan Murdoch
Paul
Luke, are you going to look at this, or should I?
Duncan Murdoch
setMethod(show, Person, function(object) {
for an object of class Person for example.
Dave
On Tue, Jun 30, 2015 at 10:11 AM, luke-tier...@uiowa.edu wrote:
Same thing happens with S3 if you redefine print(). I thought that
code was actually calculating the function to call rather than the
symbol to use, but apparently not. Shouldn't be too hard to fix.
luke
On Tue, 30 Jun 2015, Hadley Wickham wrote:
On Tue, Jun 30, 2015 at 2:20 PM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
On 30/06/2015 1:57 PM, Hadley Wickham wrote:
A slightly simpler formulation of the problem is:
show - function(...) stop(My show!)
methods::setClass(Person, slots = list(name = character))
methods::new(Person, name = Tom)
# Error in (function (...) : My show!
Just to be clear: the complaint is that the auto-called show() is not
methods::show? I.e. after
x - methods::new(Person, name = Tom)
you would expect
show(x)
to give the error, but not
x
??
Correct - I'd expect print() to always call methods::show(), not
whatever show() is first on the search path.
Hadley
--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics andFax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke-tier...@uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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Re: [Bioc-devel] rtracklayer bug?
I will add ... to the httpGet call.
On Tue, Jun 30, 2015 at 10:10 AM, Marc Carlson mcarl...@fredhutch.org wrote:
Hi Arne,
So this time when I look at the bioc-devel email list, I don't see a record
for this last name (or this email). In fact the only way I could be sure it
was you was that your post was the same... ;) If you want to post from
gmail, then you will need to subscribe the gmail address to the list here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Marc
On 06/30/2015 02:26 AM, Arne Müller wrote:
Hello,
I think there’s a problem in UCSCSession initializer in rtracklayer:
setMethod(initialize, UCSCSession,
function(.Object, url =http://genome.ucsc.edu/cgi-bin/;,
user =ULL, session = NULL, force = FALSE, ...)
{
.Object@url - url
.Object@views - new.env()
gwURL - ucscURL(.Object, gateway)
if (force) {
gwURL - paste0(gwURL, '?redirect=anual')
}
gw - httpGet(gwURL, cookiefile =empfile(), header = TRUE,
.parseúLSE)
if (grepl(redirectTd, gw)) {
url - sub(.*?a href=h([^[:space:]]+cgi-bin/).*,
h\\1, gw)
return(initialize(.Object, url, user=er, session=session,
force=UE, ...))
}
cookie - grep(Set-[Cc]ookie: hguid[^==, gw)
if (!length(cookie))
stop(Failed to obtain 'hguid' cookie)
hguid - sub(.*Set-Cookie: (hguid[^==[^;]*);.*, \\1, gw)
.Object@hguid - hguid
if (!is.null(user) !is.null(session)) { ## bring in other
session
ucscGet(.Object, tracks,
list(hgS_doOtherUser =submit, hgS_otherUserName
user,
hgS_otherUserSessionName =ession))
}
.Object
})
Shouldn’t ‘…’ be passed to httpGet that in turn is passed to
RCURL, I.e.
gw - httpGet(gwURL, cookiefile =empfile(), header = TRUE,
.parseúLSE, …) ?
We run an internal instance of the UCSC genome browser and need to pass a
cookie to all http-requests. The problem is that
session =ew ('UCSCSession', url=myInternalURL, cookie=myAuthCookie)
Does not pass the ‘cookie’ argument to httpGet.
Regards,
Arne
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[Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?
Hi r-devel
If you define a function named `show` or attach a package with an exported
`show` function, then printing/vieweing S4 objects breaks. This is probably
because the `print` function calls `show`, which is now masked.
Example:
show - function() {}
setClass(Person, slots = list(name = character))
tom - new(Person, name = Tom)
tom # error
methods::show(tom) # works
The error was a surprise to me because I was under the assumption that
`show` would be namespaced and therefore should not break.
I'm wondering if this is intended behaviour, or if this is a problem. My
intuition, and Hadley agreed on Twitter, is that defining a `show` method
should not have such a grave effect on printing S4 objects.
Thanks
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Re: [Rd] Guidelines for S3 regression models
Given how much documentation is available on R coding in general, it is surprising how little is available specifically on writing model code. Researchers who come up with a new method of regression, and who want to write an S3 model for that method, must currently go all the way back to the Venables and Ripley S programming book. On 26.06.2015 14:09, Stephen Milborrow wrote: Once we have built a regression model, we typically want to use the model for further processing, such as making predictions from the model or plotting the residuals. Unfortunately, for many packages on CRAN this can be difficult. For example, some models don't have a residuals method and don't save the call or data --- so you can't tell how to generate the residuals from the model object itself. A common snag is that for some models the new data for predict() has to be a matrix; for others it has to be a data.frame. This places an unnecessary burden on the user when both data.frames and matrices can easily be supported by predict. To mitigate such issues, I'm going out on a limb and presenting some guidelines for writers of S3 regression model functions (this document is currently part of the plotmo package): http://www.milbo.org/doc/modguide.pdf On 26.06.2015 16:41, Achim Zeileis wrote: I think this is a nice and useful starting point. It's probably not comprehensive (yet) but will surely help. You could add something more about writing the formula interface and the correct processing of model.frame, terms, model.response, model.matrix, model.weights, model.offset. Especially for models with linear predictors the latter two can be very useful and are often not hard to implement. In case the model has multiple parts or multiple responses, the Formula package (and its vignette) might also be helpful. As for the S3 methods, I would omit coefficients, fitted.values, and resid from the list. These dispatch to coef, fitted, and residuals anyway. For inference it would also be very useful to add nobs(), df.residual(), vcov(), and logLik() and/or deviance() where applicable. An overview which lists some (but not all) useful methods is in Table 1 of vignette(betareg, package = betareg). For coef() and vcov() it is useful/important that the names and dimension match. Then Wald tests can be easily computed in functions like car::linearHypothesis(), car::deltaMethod(), lmtest::waldtest(), or lmtest::coeftest(). Thanks for these, I'll update the document. Stephen Milborrow __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
