Re: [Rd] Box.test reference correction (PR#13554)
Thank you, incorporated now. (My memory says we've been here before, so perhaps the correction did not get picked up last time around.) On Tue, 24 Feb 2009, soly...@stat.math.ethz.ch wrote: Full_Name: Peter Solymos Version: 2.8.1 OS: Windows Submission from: (NULL) (129.128.141.92) The help page of the Box.test function (stats) states that the Ljung-Box test was published in: Ljung, G. M. and Box, G. E. P. (1978), On a measure of lack of fit in time series models. Biometrika 65, 553--564. The page numbers are incorrect. The correct citation should be as follows: Ljung, G. M. and Box, G. E. P. (1978), On a measure of lack of fit in time series models. Biometrika 65, 297--303. Yours, Peter __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] learning R
a quick follow-up: e = new.env() e$a = 1 names(e) # NULL names(e) = 'a' # error in names(e) = "foo" : names() applied to a non-vector this is surprising. names(e) 'works', there is no complaint, but when names<- is used, the error is about the use of names, not names<-. btw. ?names says: "Description: Functions to get or set the names of an object. Usage: names(x) names(x) <- value Arguments: x: an R object. " and there is no clarification in the rest of the page that x cannot be an environment, or that it has to be a vector. furthermore: p = pairlist(a=1) names(p) # "a" names(p) = 'b' # fine is.vector(p) # FALSE which is incoherent with the above error message, in that p is *not* a vector. vQ Wacek Kusnierczyk wrote: > > the following: > > names(a[2]) = 'foo' > > has (partially) a functional flavour, in that you assign to the names of > a *copy* of a part of a, while > > names(a)[2] = 'foo' > > does not have the flavour, in that you assign to the names of a; it > seems, according to the man page you quote, to be equivalent to: > > a = 'names<-'(a, '[<-.'(names(a), 2, 'foo')) > > which proceeds as follows: > > tmp1 = names(a) > # get a copy of the names of a, no effect on a > > tmp2 = '[<-'(tmp1, 2, 'foo') > # get a copy of tmp1 with the second element replaced with 'foo' > # no effect on either a or tmp1 > > tmp3 = 'names<-'(a, tmp2) > # get a copy of a with its names replaced with tmp2 > # no effect on either a, tmp1, or tmp2 > > a = tmp3 > # backassign the result to a > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] Semantics of sequences in R
Berwin A Turlach wrote: on the other hand, i have seen quite a few responses that were bashing a user for reporting a non-existent bug or submitting an annoying patch. >>> In didactic terms those are "negative motivations/reinforcements"; >>> opinion differ on how effective they are to reach certain learning >>> outcomes. >>> >>> >> ah, so what's the difference between the way i pinpoint design flaws >> and the way r gurus respond to people, so that i am running with a >> chip on my shoulder, and they are being 'negatively >> motivating/reinforcing' in didactic terms? [...] >> > > Your goal is, presumably, that you want to have the design flaws > fixed/discussed/&c. The goal of the R gurus is to avoid having to > waste their time on unproductive issues because people do not read > documentation/behave contrary to how they are asked to behave/&c. > > To reach your goal, the controversial approach is counter productive. > To reach their goal, the controversial approach can be quite effective. > berwin, i have an additional reflection which i'd like to share with thee. glad to see thy opinion. there certainly is a difference between the r gurus who develop and maintain an impressive software system, and the average user who has limited understanding of both the internals and the interface. but this difference is in the amount of knowledge about this specific product; in interpersonal communication, the developers and the users are essentially *peers*. offline, i have been told that some of the r gurus can be equally arrogant (read: negatively motivating/reinforcing) to other developers as they are to users; but why should a user care, especially that there is no hierarchical dependence between the developers and the users, while there may be between the developers? (which would still not justify arrogance, but some bosses just cannot let it be.) when you seem to sanction and support the rudeness with which some r gurus tend to respond to certain posts, and which is clearly documented in a number of fortunes, you have no point in objecting to how certain users write to you. irrespectively of your achievements with r, you are due to all users the same respect you expect to be treated with. to paraphrase from duncan's, you cannot demand anything from the users, and if you expect them to be kind, be kind too. or live with it. vQ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] learning R
Hi Wacek: Somewhere I remember reading that environments have functionality like lists EXCEPT for the names part. IIRC, I think that I read this in the R Language Reference manual also. On Wed, Feb 25, 2009 at 4:32 AM, Wacek Kusnierczyk wrote: a quick follow-up: e = new.env() e$a = 1 names(e) # NULL names(e) = 'a' # error in names(e) = "foo" : names() applied to a non-vector this is surprising. names(e) 'works', there is no complaint, but when names<- is used, the error is about the use of names, not names<-. btw. ?names says: "Description: Functions to get or set the names of an object. Usage: names(x) names(x) <- value Arguments: x: an R object. " and there is no clarification in the rest of the page that x cannot be an environment, or that it has to be a vector. furthermore: p = pairlist(a=1) names(p) # "a" names(p) = 'b' # fine is.vector(p) # FALSE which is incoherent with the above error message, in that p is *not* a vector. vQ Wacek Kusnierczyk wrote: the following: names(a[2]) = 'foo' has (partially) a functional flavour, in that you assign to the names of a *copy* of a part of a, while names(a)[2] = 'foo' does not have the flavour, in that you assign to the names of a; it seems, according to the man page you quote, to be equivalent to: a = 'names<-'(a, '[<-.'(names(a), 2, 'foo')) which proceeds as follows: tmp1 = names(a) # get a copy of the names of a, no effect on a tmp2 = '[<-'(tmp1, 2, 'foo') # get a copy of tmp1 with the second element replaced with 'foo' # no effect on either a or tmp1 tmp3 = 'names<-'(a, tmp2) # get a copy of a with its names replaced with tmp2 # no effect on either a, tmp1, or tmp2 a = tmp3 # backassign the result to a __ r-h...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] invalid comparison in numeric sequence (PR#13551)
alexandre.court...@gmail.com wrote: > >> 0.6==0.6 > [1] TRUE >> seq(0,1,0.1)==0.4 > [1] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE >> seq(0,1,0.1)==0.6 > [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE >> seq(0,1,0.1)==0.8 > [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE > > > What is wrong with 0.6 ??? (TRUE is missing) > I tried 3 differents computers (2 Ubuntu with R 2.8.1, and one Mac with R > 2.8). FAQ 7.31, not a bug. Expect about 10 people to tell you so. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] S4 helper functions: regular or generic?
Hi there, I want to write helper functions for a base class, which will be used by its subclasses in the S4 world. This function ___will___ update certain slots of its argument object. Please help me decide which one of the following is a better approach with respect to coding style, memory usage and speed: o Write a regular function. o Declare a generic and implement it just for the base class. Thanks for sharing your insight and time, gopi. http://gopi-goswami.net/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] length 1 offset in glm (& lm)
This post about length 1 offsets on R help seems to have been ignored (sorry deleted original email - is there a way to continue thread in this case?) https://stat.ethz.ch/pipermail/r-help/2009-February/189352.html It does seem to be a bug, in that glm does not behave as documented. In fact the same bug applies to lm as well. I don't think the suggested fix works though - Y isn't available until the model frame is evaluated. Moreover you would want to evaluate the offset as part of the model frame, to take care of the search path, subset and na.action. One possibility would be to modify model.frame to recycle variables of length one. This would be a potentially useful feature from my point of view as offset(constant) could replace Const(constant) in gnm, which is basically a work around for this problem in the case of specifying a constant in a nonlinear term. However, this solution may have undesired side-effects and I don't feel too strongly about it as there are various work-arounds. Perhaps the simplest solution would be to modify the docs so that offsets of length one are disallowed - it is easy enough for the user to create a vector of the right length as necessary. Best regards, Heather __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] length 1 offset in glm (& lm)
On Wed, 25 Feb 2009, Kenneth Knoblauch wrote:
Hi
Quoting Prof Brian Ripley :
On Wed, 25 Feb 2009, Heather Turner wrote:
This post about length 1 offsets on R help seems to have been ignored
(sorry deleted original email - is there a way to continue thread in
this case?)
https://stat.ethz.ch/pipermail/r-help/2009-February/189352.html
So let's be clear: this was the 'offset' argument' and not the offset()
function as you refer to below.
It occurs for both
Yes (I knew). but no one (AFAICS) said the function allows length-1
arguments: Heather is raising the possibility that it should as new
functionality, I believe.
c1 <- structure(list(Contr = c(0.028, 0.043, 0.064, 0.097, 0.146, 0.219
), Correct = c(34L, 57L, 94L, 152L, 160L, 160L), Incorrect = c(126L,
103L, 66L, 8L, 0L, 0L)), .Names = c("Contr", "Correct", "Incorrect"
), row.names = c(NA, 6L), class = "data.frame")
glm(cbind(Correct, Incorrect) ~ Contr + offset(qlogis(0.25)) - 1, binomial,
data = c1)
Error in model.frame.default(formula = cbind(Correct, Incorrect) ~ Contr + :
variable lengths differ (found for 'offset(qlogis(0.25))')
+
Thanks for looking into this when time permits.
Ken
--- remaining deleted
--
Ken Knoblauch
Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr/members/kenneth-knoblauch.html
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] length 1 offset in glm (& lm)
Prof Brian Ripley wrote: > On Wed, 25 Feb 2009, Kenneth Knoblauch wrote: > >> Hi >> >> Quoting Prof Brian Ripley : >> >>> On Wed, 25 Feb 2009, Heather Turner wrote: >>> This post about length 1 offsets on R help seems to have been ignored (sorry deleted original email - is there a way to continue thread in this case?) https://stat.ethz.ch/pipermail/r-help/2009-February/189352.html >>> >>> So let's be clear: this was the 'offset' argument' and not the offset() >>> function as you refer to below. >> >> It occurs for both > > Yes (I knew). but no one (AFAICS) said the function allows length-1 > arguments: Heather is raising the possibility that it should as new > functionality, I believe. Makes sense to have them consistent though, and we we do advertise that recycling works for the argument. Looks like this could be fixed at the level of model.frame.default, but the sticky bit is where to get the repeat count in case the formula is something like "~-1". I don't quite fathom the current rules: > model.frame(~-1,offset=1) (offset) 11 > model.frame(~-1,offset=1,data=aq) (offset) 11 > model.frame(Ozone~-1,offset=1,data=aq) Error in model.frame.default(Ozone ~ -1, offset = 1, data = aq) : variable lengths differ (found for '(offset)') > model.frame(Ozone~-1,data=aq) Ozone 141 236 312 418 628 > model.frame(~-1,data=aq) data frame with 0 columns and 6 rows > foo <- 2:3 > model.frame(~foo-1,data=aq) foo 12 23 3 4 5 6 Warning message: In format.data.frame(x, digits = digits, na.encode = FALSE) : corrupt data frame: columns will be truncated or padded with NAs > foo <- 2 > model.frame(~foo-1,data=aq) foo 1 2 -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] length 1 offset in glm (& lm)
Prof Brian Ripley wrote:
> On Wed, 25 Feb 2009, Kenneth Knoblauch wrote:
>
>> Hi
>>
>> Quoting Prof Brian Ripley :
>>
>>> On Wed, 25 Feb 2009, Heather Turner wrote:
>>>
This post about length 1 offsets on R help seems to have been ignored
(sorry deleted original email - is there a way to continue thread in
this case?)
https://stat.ethz.ch/pipermail/r-help/2009-February/189352.html
>>>
>>> So let's be clear: this was the 'offset' argument' and not the offset()
>>> function as you refer to below.
>>
>> It occurs for both
>
> Yes (I knew). but no one (AFAICS) said the function allows length-1
> arguments: Heather is raising the possibility that it should as new
> functionality, I believe.
>
Not particularly, just observing that if the problem of handling a
length one offset passed to the offset argument is solved by model.frame
doing the necessary recycling, then offset() would also work with length
one arguments (I think) and this could be a useful feature. If the
problem is solved by dealing with the offset argument separately, then
you wouldn't get this side-benefit, so it's just something to bear in
mind when deciding on a fix.
>> c1 <- structure(list(Contr = c(0.028, 0.043, 0.064, 0.097, 0.146, 0.219
>> ), Correct = c(34L, 57L, 94L, 152L, 160L, 160L), Incorrect = c(126L,
>> 103L, 66L, 8L, 0L, 0L)), .Names = c("Contr", "Correct", "Incorrect"
>> ), row.names = c(NA, 6L), class = "data.frame")
>>
>> glm(cbind(Correct, Incorrect) ~ Contr + offset(qlogis(0.25)) - 1,
>> binomial,
>> data = c1)
>> Error in model.frame.default(formula = cbind(Correct, Incorrect) ~
>> Contr + :
>> variable lengths differ (found for 'offset(qlogis(0.25))')
>> +
>>
>> Thanks for looking into this when time permits.
>>
>> Ken
>>
>> --- remaining deleted
>
>> --
>> Ken Knoblauch
>> Inserm U846
>> Stem-cell and Brain Research Institute
>> Department of Integrative Neurosciences
>> 18 avenue du Doyen Lépine
>> 69500 Bron
>> France
>> tel: +33 (0)4 72 91 34 77
>> fax: +33 (0)4 72 91 34 61
>> portable: +33 (0)6 84 10 64 10
>> http://www.sbri.fr/members/kenneth-knoblauch.html
>>
>
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] invalid comparison in numeric sequence (PR#13551)
This is one of the joys of floating point arithmetic. Look at the 7th element of seq(0,1,.1) - 0.6 Also, check the all.equal(x,y,tolerance=epsilon ) function. John -r-devel-boun...@r-project.org wrote: - To: r-de...@stat.math.ethz.ch From: alexandre.court...@gmail.com Sent by: r-devel-boun...@r-project.org Date: 02/24/2009 08:55AM cc: r-b...@r-project.org Subject: [Rd] invalid comparison in numeric sequence (PR#13551) Full_Name: alex Version: 2.8.1 OS: Ubuntu / MacOSX Submission from: (NULL) (162.38.183.51) > 0.6==0.6 [1] TRUE > seq(0,1,0.1)==0.4 [1] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE > seq(0,1,0.1)==0.6 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE > seq(0,1,0.1)==0.8 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE What is wrong with 0.6 ??? (TRUE is missing) I tried 3 differents computers (2 Ubuntu with R 2.8.1, and one Mac with R 2.8). __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] length 1 offset in glm (& lm)
On Wed, 25 Feb 2009, Heather Turner wrote: This post about length 1 offsets on R help seems to have been ignored (sorry deleted original email - is there a way to continue thread in this case?) https://stat.ethz.ch/pipermail/r-help/2009-February/189352.html So let's be clear: this was the 'offset' argument' and not the offset() function as you refer to below. It does seem to be a bug, in that glm does not behave as documented. In fact the same bug applies to lm as well. Not ignored, just not yet resolved so nothing really useful to say as yet. I suspect the documentation was once correct but the offset argument had some rather undesirable prperties at the time. And there appears to be some legacy code to do the recycling. So quite a bit of work is needed on the history to deal wth what is rather a small point: sorting out some problems with failing packages (rgdal and friends) has been a much higher priority (let alone the day jobs). I don't think the suggested fix works though - Y isn't available until the model frame is evaluated. Moreover you would want to evaluate the offset as part of the model frame, to take care of the search path, subset and na.action. That used not to be the case for the offset _argument_, so probably where the docs came from. One possibility would be to modify model.frame to recycle variables of length one. This would be a potentially useful feature from my point of view as offset(constant) could replace Const(constant) in gnm, which is basically a work around for this problem in the case of specifying a constant in a nonlinear term. However, this solution may have undesired side-effects and I don't feel too strongly about it as there are various work-arounds. Perhaps the simplest solution would be to modify the docs so that offsets of length one are disallowed - it is easy enough for the user to create a vector of the right length as necessary. Best regards, Heather __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] S4 helper functions: regular or generic?
Hi Gopi -- Gopi Goswami writes: > Hi there, > > > I want to write helper functions for a base class, which will be used > by its subclasses in the S4 world. This function ___will___ update > certain slots of its argument object. Please help me decide which one > of the following is a better approach with respect to coding style, > memory usage and speed: > My opinion: > o Write a regular function. memory and speed > o Declare a generic and implement it just for the base class. coding 'style', but style is subjective. There are other aspects of S4, e.g., type checking, method dispatch, programmatically defined and discoverable API, ... (positives), cumbersome documentation (negative). My usual pattern of development is to be seduced by the siren of speed, only to regret boxing myself in. I find that my S4 objects typically serve as containers for coordinating other entities. The important methods typically extract R 'base' objects from the S4 class, manipulate them, and repackage the result as S4. The time and speed issues are in the manipulation, not in the extraction / repackaging. This is contrast to, say, an implementation of a tree-like data structure with a collection of 'Node' objects, where tree operations would require access to each object and would be horribly slow in S4 (and perhaps R when nodes were represented as a list, say, at least compared to a C-level representation, or an alternative representation that took advantage of R's language characteristics). Martin > > Thanks for sharing your insight and time, > gopi. > http://gopi-goswami.net/ > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] length 1 offset in glm (& lm)
Some digging showed that this has not worked for a long time and the documentation is either legacy or wishful thinking. So for R-patched the right approach is to fix the documentation and I will do so shortly. As for model.frame() recycling: that sounds an appealing idea and I don't think I would want to confine it to case of length one: exact repeats recycling are allowed in a number of places. And re Peter's example, this could be done only when it is unambiguous, or only where there is a response or But that will have to wait for another day (or another hand). On Wed, 25 Feb 2009, Prof Brian Ripley wrote: On Wed, 25 Feb 2009, Heather Turner wrote: This post about length 1 offsets on R help seems to have been ignored (sorry deleted original email - is there a way to continue thread in this case?) https://stat.ethz.ch/pipermail/r-help/2009-February/189352.html So let's be clear: this was the 'offset' argument' and not the offset() function as you refer to below. It does seem to be a bug, in that glm does not behave as documented. In fact the same bug applies to lm as well. Not ignored, just not yet resolved so nothing really useful to say as yet. I suspect the documentation was once correct but the offset argument had some rather undesirable prperties at the time. And there appears to be some legacy code to do the recycling. So quite a bit of work is needed on the history to deal wth what is rather a small point: sorting out some problems with failing packages (rgdal and friends) has been a much higher priority (let alone the day jobs). I don't think the suggested fix works though - Y isn't available until the model frame is evaluated. Moreover you would want to evaluate the offset as part of the model frame, to take care of the search path, subset and na.action. That used not to be the case for the offset _argument_, so probably where the docs came from. One possibility would be to modify model.frame to recycle variables of length one. This would be a potentially useful feature from my point of view as offset(constant) could replace Const(constant) in gnm, which is basically a work around for this problem in the case of specifying a constant in a nonlinear term. However, this solution may have undesired side-effects and I don't feel too strongly about it as there are various work-arounds. Perhaps the simplest solution would be to modify the docs so that offsets of length one are disallowed - it is easy enough for the user to create a vector of the right length as necessary. Best regards, Heather __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] invalid comparison in numeric sequence (PR#13551)
> > seq(0,1,0.1)==0.4 > [1] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE > > seq(0,1,0.1)==0.6 > [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE > > seq(0,1,0.1)==0.8 > [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE > > What is wrong with 0.6 ??? (TRUE is missing) > I tried 3 differents computers (2 Ubuntu with R 2.8.1, and one Mac with R > 2.8). If you know that all the numbers in a sequence should have a given decimal precision, then you obtain a better result using round(,digits=...). For example, x <- round(seq(0,1,0.1), digits=1) rbind(x == 0.4, x == 0.6, x ==0.8) produces [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [1,] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE [2,] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE [3,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE This does not mean, that x[7] is now equal to 0.6, however both x[7] and 0.6 are represented by the same 53-bit floating point number formatC(x[7], digits=20) # "0.5999778" formatC(0.6, digits=20) # "0.5999778" Petr. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Unexpected side effect of the ":::" operator on the value of isGeneric
Hi,
when running the following on a fresh R,
library("IRanges")
annotation
showMethods("annotation")
Biobase:::annotation
showMethods("annotation")
I get (see the "^" marked output at the bottom):
> library("IRanges")
Carico il pacchetto richiesto: 'IRanges'
The following object(s) are masked from package:base :
cbind,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rbind,
rep.int,
table
> annotation
standardGeneric for "annotation" defined from package "IRanges"
function (x, ...)
standardGeneric("annotation")
Methods may be defined for arguments: x
Use showMethods("annotation") for currently available ones.
> showMethods("annotation")
Function: annotation (package IRanges)
x="AnnotatedList"
> Biobase:::annotation
standardGeneric for "annotation" defined from package "Biobase"
function (object)
standardGeneric("annotation")
Methods may be defined for arguments: object
Use showMethods("annotation") for currently available ones.
> showMethods("annotation")
Function "annotation":
^^^
It seems that the value of isGeneric("annotation"), when it is called
within showMethods, is FALSE, while it is TRUE when called outside.
> sessionInfo()
R version 2.9.0 Under development (unstable) (2009-02-25 r48007)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=C;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] IRanges_1.1.40
loaded via a namespace (and not attached):
[1] Biobase_2.3.10
Best wishes
Wolfgang
--
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
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Re: [Rd] [R] make check reg-tests-1.R error on solaris
Do you have a ZFS file system? That seems to be the common factor
where people have actually told us. However, other Solaris
9/10/OpenSolaris systems work, as you will see from the R-admin
manual. We cannot help with errors we cannot reproduce: rather we
need someone with the problem to help us.
Such questions are far more apporpriate to the R-devel list: see the
posting guide. So I have diverted this there.
On Wed, 25 Feb 2009, Karen Noel wrote:
R 2.5.1 compiled, passed the make check and has been successfully running for
a couple years on a Sun Fire V490 running Solaris 9. I need a newer version
of R, but can't get a newer version of R to pass the make check. I've tried
2.8.1, 2.7.2, 2.6.2 and 2.6.0. (2.5.1 still passes on this server) At this
point I thought I'd try to compile it on another Sun server (Solaris 10), but
it had the same problem. Configuring with no options didn't help. I commented
out the failed test from the Makefile to see if it would pass the rest of the
tests. It passes all the rest of the tests. Here is the failure error from
make check.
make[2]: Entering directory `/usr/local/src/R-2.8.1/tests'
running regression tests
make[3]: Entering directory `/usr/local/src/R-2.8.1/tests'
running code in 'reg-tests-1.R' ...make[3]: *** [reg-tests-1.Rout] Error 1
make[3]: Leaving directory `/usr/local/src/R-2.8.1/tests'
make[2]: *** [test-Reg] Error 2
make[2]: Leaving directory `/usr/local/src/R-2.8.1/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/usr/local/src/R-2.8.1/tests'
make: *** [check] Error 2
bash-2.05#
Here is output from reg-tests-1.Rout.fail.
[1] "41c6167e" "dir1" "dir2" "dirs"
"file275c23f2"
[6] "file33f963f2" "moredirs"
file.create(file.path(dd, "somefile"))
[1] TRUE TRUE TRUE TRUE
dir(".", recursive=TRUE)
[1] "41c6167e" "dir1/somefile" "dir2/somefile"
[4] "dirs/somefile" "file275c23f2" "file33f963f2"
[7] "moredirs/somefile"
stopifnot(unlink("dir?") == 1) # not an error
Error: unlink("dir?") == 1 is not TRUE
Execution halted
rm: Cannot remove any directory in the path of the current working directory
/tmp/RtmprBjF6W
Looking through the archives I did find a couple other people with this
error, both running Solaris 10. PR#10501 and PR#11738 have quite a lot of
information about this error, but I don't see any resolution for them.
This looks like it could possibly be enough of a problem that I haven't put
2.8.1 in production. Can you help me with a resolution or let me know if it
is safe to ignore? I'd appreciate it.
Thank you!
Karen
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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