Re: [Rd] Bug in merge() in R-2.0.0 alpha
On Wed, 15 Sep 2004, Uwe Ligges wrote:
> In some cases, merge() has a problem in R-2.0.0 alpha (2004-09-14):
>
>x <- structure(c("a", "b", "2", "0.2-26", "O", "O"), .Dim = c(2, 3),
> .Dimnames = list(c("1", "2"), c("P", "V", "2")))
>
>y <- structure(c("a", "b", "2", "0.2-25", "O", "O"), .Dim = c(2, 3),
> .Dimnames = list(c("1", "2"), c("P", "V", "1")))
>
>merge(x, y, all.y=TRUE)
>
> Error in "[<-"(`*tmp*`, ri, value = NULL) :
> incompatible types
>
>
> Looks like the NA handling has changed anywhere.
Peter was right. rbind.data.frame had
## copy names if any
names(value[[jj]])[ri] <- names(xj)
but did not test if there were any. It would probably be a good idea if
that did work but for now I have added a test.
--
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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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FW: [Rd] Parsing multi-line strings. Bug? Feature?
> Kevin Wright <[EMAIL PROTECTED]> writes: > > > R 1.9.1 requires multi-line strings to contain a backslash at the > > end of each line (except the last line). As noted by Mark > > Bravington (http://tolstoy.newcastle.edu.au/R/help/02b/5199.html) > > this requirement appears to be undocumented. > > > > In S-Plus 6.2, multi-line strings do not need a backslash for continuation. > > > > I recently (http://tolstoy.newcastle.edu.au/R/devel/04b/0256.html) > > requested compatability with S-Plus and was told to contribute > > a patch and then it would be considered. Here is the proposed patch. <> > > Thanks for considering this patch. > > Peter Dalgaard wrote: > Sorry, I don't think that is good enough (notwithstanding the > nonstandard comment character). Notice that Splus does this: > > > x <- "foo > Continue string: bar > Continue string: baz" > > (and the entry is interruptible with Ctrl-C too) > > There's a very good reason for the change of prompt, as anyone who has > debugged SAS code with stray quotes will tell you: The system would > appear to be completely unresponsive because all input is being eaten > by the string readers. I think the following patch in StringValue might address Peter Dalgaard's point: when a bare newline is found (i.e. not preceded by a backslash), it's pushed back onto the character stack via xxungetc(c) and StringValue pretends that it's just read a backslash instead. Then, as usual, it looks for the next character which is of course a newline, and proceeds as normal. Output is from diff gram.c on R-devel from 7/9/2004. I hope the comments look sufficiently standard now (I'm not a C programmer). Mark 3122a3123,3124 > /* Old behaviour was: return ERROR; */ > /* Now pretend there was a backslash before EOL */ 3124c3126 < return ERROR; --- > c = '\\'; > *** Mark Bravington CSIRO (CMIS) PO Box 1538 Castray Esplanade Hobart TAS 7001 phone (61) 3 6232 5118 fax (61) 3 6232 5012 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] cor() fails with big dataframe
Hello,
I have a big dataframe with *NO* na's (9 columns, 293380 rows).
# doing
memory.limit(size = 10)
cor(x)
#gives
Error in cor(x) : missing observations in cov/cor
In addition: Warning message:
NAs introduced by coercion
#I found the obvious workaround:
COR <- matrix(rep(0, 81),9,9)
for (i in 1:9) for (j in 1:9) {if (i>j) COR[i,j] <- cor (x[,i],x[,j])}
#which works fine, with no warning
#looks like a "cor()" bug.
#I checked absence of NA's by
x <- x[complete.cases(x),]
summary(x)
apply(x,2, function (x) (sum(is.na(x
#I use R 1.9.1
Cheers,
Mayeul KAUFFMANN
Université Pierre Mendès France
Grenoble - France
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Re: [Rd] Bug in merge() in R-2.0.0 alpha
Uwe Ligges <[EMAIL PROTECTED]> writes:
> In some cases, merge() has a problem in R-2.0.0 alpha (2004-09-14):
>
>x <- structure(c("a", "b", "2", "0.2-26", "O", "O"), .Dim = c(2, 3),
> .Dimnames = list(c("1", "2"), c("P", "V", "2")))
>
>y <- structure(c("a", "b", "2", "0.2-25", "O", "O"), .Dim = c(2, 3),
> .Dimnames = list(c("1", "2"), c("P", "V", "1")))
>
>merge(x, y, all.y=TRUE)
>
> Error in "[<-"(`*tmp*`, ri, value = NULL) :
> incompatible types
>
>
> Looks like the NA handling has changed anywhere.
Names handling, more likely:
> v <- structure(list("2" = NA), .Names = "2", class = "data.frame", row.names = "2")
> u <- structure(list("2" = structure(1, .Names = "1", .Label = "O", class =
> "factor")), .Names = "2", class = "data.frame", row.names = "1")
> uu <- structure(list("2" = structure(1, .Label = "O", class = "factor")), .Names =
> "2", class = "data.frame", row.names = "1")
> rbind(v,u)
2
2
1O
> rbind(v,uu)
2
2
1O
> rbind(u,v)
Error during wrapup: incompatible types
> rbind(uu,v)
2
1O
2
(Notice that the only difference between u and uu is the .Names bit)
--
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c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [Rd] file.info() on file larger than 2GB
This appears to be fairly easy to solve, at least on Linux. R-devel now
has an option --enable-linux-lfs that sets up the appropriate flags (and a
very few other code changes were needed). Similar options work on
Solaris.
I have been able to create a 2.5Gb text file, move around it and read
lines from here and there including near the end, both as a plain file and
as a gzip-ed file. And file.info reports correctly.
On Tue, 31 Aug 2004, Prof Brian Ripley wrote:
> This is a purely OS issue: your OS has not been set up so the fopen and
> stat calls handle > 2Gb files. There is one R issue: the size will
> overflow in file.info.
>
> For example, under Solaris 64-bit applications can handle such files
> whereas 32-bit ones need calls to stat64, fopen64 etc.
>
> It seems a very exotic need, but if someone wants to find out how to use
> the OS-specific ways to extend stat etc and supply patches, please do so.
>
> We don't put OS-specific limitations on help pages.
>
> On Tue, 31 Aug 2004, Roger D. Peng wrote:
>
> > I've got a file that's approximately 2.2GB and it seems to be foiling
> > file.info(). When I run `stat' from the shell I get
> >
> > zooey:> stat data.csv
> >File: `data.csv'
> >Size: 2271197563 Blocks: 4440280IO Block: 4096 regular file
> > Device: 342h/834d Inode: 9994308 Links: 1
> > Access: (0644/-rw-r--r--) Uid: ( 500/ rpeng) Gid: ( 500/ rpeng)
> > Access: 2004-08-31 09:50:04.0 -0400
> > Modify: 2004-08-26 19:09:42.0 -0400
> > Change: 2004-08-31 09:53:29.0 -0400
>
> Take a look at the source code for stat, in coreutils.
>
> > But, file.info() in R-devel gives me:
> >
> > > file.info("data.csv")
> > size isdir mode mtime ctime atime uid gid uname grname
> > data.csv NANA NA NA
> >
> > I assume this has something to do with the underlying call to `stat'
> > in `do_fileinfo'.
> >
> > This alone is not much of a problem but I also can't seem to be able
> > to open a file connection to the same file. For example,
> >
> > > con <- file("data.csv")
> > > open(con, "r")
> > Error in open.connection(con, "r") : unable to open connection
> > In addition: Warning message:
> > cannot open file `data.csv'
> >
> > Also, interestingly,
> >
> > > file.exists("data.csv")
> > [1] FALSE
> >
> > I take it all these things are related.
> >
> > Is it possible to fix this within R? Or should there be a note in the
> > help pages?
> >
> > > version
> > _
> > platform i686-pc-linux-gnu
> > arch i686
> > os linux-gnu
> > system i686, linux-gnu
> > status Under development (unstable)
> > major2
> > minor0.0
> > year 2004
> > month08
> > day 31
> > language R
> >
> > -roger
> >
> > __
> > [EMAIL PROTECTED] mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
>
>
--
Brian D. Ripley, [EMAIL PROTECTED]
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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Re: [Rd] prototype in setClass.
It works better if you give setClass the right arguments.
In your second call, you omitted the representation= argument, so you
need to name the prototype argument:
setClass("AtomList"
,contains="List"
,prototype =
prototype(content="Atom")## would like
to specify this
)
With this change:
R> new("AtomList")
An object of class "AtomList"
list()
Slot "uniq":
[1] FALSE
Slot "content":
[1] "Atom"
(We can probably do some bullet-proofing, since the object returned from
prototype() has a specific class, but that may have to wait until
2.0.1.)
Wolski wrote:
>
> Hi!
>
> To specify a prototype in the setClass declaration is a great feature.
> But prototype seems no to work for slots of the "super" class.
> eg. The following code is declaring first the super class "List". This class has a
> slot "content".
> The class "AtomList" inherits from it and I would like to set content="Atom" by
> prototype(content="Atom").
> But after new("AtomList") is called the slot content is empty as you can see running
> the code below.
>
> setClass("List"
> ,representation(
> uniq="logical"
> ,content="character" # would
> like to set this when declaring the inheriting class.
> ,names="character")
> ,contains="list"
> ,prototype(uniq=FALSE)
> )
>
> setClass("AtomList"
> ,contains="List"
> ,prototype(content="Atom")## would like to
> specify this
> )
>
> new("AtomList")
>
> An object of class "AtomList"
> list()
> Slot "uniq":
> [1] FALSE
>
> Slot "content":
> character(0)
> ###<-still not specified even if provided in prototype.
>
> Slot "names":
> character(0)
>
> Version:
>
> R : Copyright 2004, The R Foundation for Statistical Computing
> Version 2.0.0 alpha (2004-09-14), ISBN 3-900051-07-0
> or
> R1.9.1 patched.
>
> /E
>
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--
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Bell Labs, Lucent Technologiesoffice: (908)582-2681
700 Mountain Avenue, Room 2C-282 fax:(908)582-3340
Murray Hill, NJ 07974web: http://www.cs.bell-labs.com/~jmc
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[Rd] Bug in merge() in R-2.0.0 alpha
In some cases, merge() has a problem in R-2.0.0 alpha (2004-09-14):
x <- structure(c("a", "b", "2", "0.2-26", "O", "O"), .Dim = c(2, 3),
.Dimnames = list(c("1", "2"), c("P", "V", "2")))
y <- structure(c("a", "b", "2", "0.2-25", "O", "O"), .Dim = c(2, 3),
.Dimnames = list(c("1", "2"), c("P", "V", "1")))
merge(x, y, all.y=TRUE)
Error in "[<-"(`*tmp*`, ri, value = NULL) :
incompatible types
Looks like the NA handling has changed anywhere.
Uwe Ligges
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