[Rd] Bug in "$<-.data.frame" yields corrupt data frame (PR#13724)
Full_Name: Steven McKinney
Version: 2.9.0
OS: Mac OS X 10.5.6
Submission from: (NULL) (142.103.207.10)
A corrupt data frame can be constructed as follows:
foo <- matrix(1:12, nrow = 3)
bar <- data.frame(foo)
bar$NewCol <- foo[foo[, 1] == 4, 4]
bar
lapply(bar, length)
> foo <- matrix(1:12, nrow = 3)
> bar <- data.frame(foo)
> bar$NewCol <- foo[foo[, 1] == 4, 4] bar
X1 X2 X3 X4 NewCol
1 1 4 7 10
2 2 5 8 11
3 3 6 9 12
Warning message:
In format.data.frame(x, digits = digits, na.encode = FALSE) :
corrupt data frame: columns will be truncated or padded with NAs
> lapply(bar, length)
$X1
[1] 3
$X2
[1] 3
$X3
[1] 3
$X4
[1] 3
$NewCol
[1] 0
The data.frame method is
> getAnywhere("$<-.data.frame" )
A single object matching '$<-.data.frame' was found It was found in the
following places
package:base
registered S3 method for $<- from namespace base
namespace:base
with value
function (x, i, value)
{
cl <- oldClass(x)
class(x) <- NULL
nrows <- .row_names_info(x, 2L)
if (!is.null(value)) {
N <- NROW(value)
if (N > nrows)
stop(gettextf("replacement has %d rows, data has %d",
N, nrows), domain = NA)
if (N < nrows && N > 0L)
if (nrows%%N == 0L && length(dim(value)) <= 1L)
value <- rep(value, length.out = nrows)
else stop(gettextf("replacement has %d rows, data has %d",
N, nrows), domain = NA)
if (is.atomic(value))
names(value) <- NULL
}
x[[i]] <- value
class(x) <- cl
return(x)
}
>
I placed a browser() command before return(x) and did some poking
around. The issue is that the example above creates an object with
N < nrows but N == 0L, so either an else clause to check for this
condition is needed, or, it appears to me, the N > 0L part of the
conditional clause needs to be moved to the next if clause.
I modified the rows
if (N < nrows && N > 0L)
if (nrows%%N == 0L && length(dim(value)) <= 1L)
to read
if (N < nrows)
if (N > 0L && nrows%%N == 0L && length(dim(value)) <= 1L)
as in
"$<-.data.frame" <-
function (x, i, value)
{
cl <- oldClass(x)
class(x) <- NULL
nrows <- .row_names_info(x, 2L)
if (!is.null(value)) {
N <- NROW(value)
if (N > nrows)
stop(gettextf("replacement has %d rows, data has %d",
N, nrows), domain = NA)
if (N < nrows)
if (N > 0L && nrows%%N == 0L && length(dim(value)) <= 1L)
value <- rep(value, length.out = nrows)
else stop(gettextf("replacement has %d rows, data has %d",
N, nrows), domain = NA)
if (is.atomic(value))
names(value) <- NULL
}
x[[i]] <- value
class(x) <- cl
return(x)
}
Now it detects the problem above:
> foo <- matrix(1:12, nrow = 3)
> bar <- data.frame(foo)
> bar$NewCol <- foo[foo[, 1] == 4, 4]
Error in `$<-.data.frame`(`*tmp*`, "NewCol", value = integer(0)) :
replacement has 0 rows, data has 3
It doesn't appear to stumble on weird data frames (these from the
?data.frame help page)
> L3 <- LETTERS[1:3]
> (d <- data.frame(cbind(x=1, y=1:10), fac=sample(L3, 10,
replace=TRUE)))
> (d0 <- d[, FALSE]) # NULL data frame with 10 rows
> (d.0 <- d[FALSE, ]) # <0 rows> data frame (3 cols)
> (d00 <- d0[FALSE,]) # NULL data frame with 0 rows
> d0$NewCol <- foo[foo[, 1] == 4, 4]
Error in `$<-.data.frame`(`*tmp*`, "NewCol", value = integer(0)) :
replacement has 0 rows, data has 10
### Catches this problem above alright.
> d.0$NewCol <- foo[foo[, 1] == 4, 4]
> d.0
[1] x y facNewCol
<0 rows> (or 0-length row.names)
### Lets the above one through alright.
> d00$NewCol <- foo[foo[, 1] == 4, 4]
>
> d00
[1] NewCol
<0 rows> (or 0-length row.names)
### Lets the above one through alright.
Would the above modification work to fix this problem?
> sessionInfo()
R version 2.9.0 (2009-04-17)
powerpc-apple-darwin8.11.1
locale:
en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] nlme_3.1-90
loaded via a namespace (and not attached):
[1] grid_2.9.0 lattice_0.17-22 tools_2.9.0
Also occurs on Windows box with R 2.8.1
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program British Columbia Cancer
Research Centre
email: smckinney +at+ bccrc +dot+ ca
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
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[Rd] Wishlist: Navigate to "Index" page of help when no topic specified (PR#13860)
Hi all,
When I install a new package, and don't yet know any function names,
I have to play the "poor man's game" to get to the standard
help system "Index" page for the package:
Poor Man's Game -=20
Load new package;=20
issue search() command;
find position (say N) of loaded package;=20
issue objects(pos =3D N) command;
get name of a random function (san newFunction);=20
issue ?newFunction command;
scroll to bottom of page;=20
click on the "Index" hyperlink
There are other variations, but they all involve this=20
long march to the Index page.
What I'd like to be able to do is enter the command
> help(package =3D "survival")
or
> ?survival::
and get the usual hyperlinked help page displayed (the "00Index" page)
instead of the static "text only" display or an error message
(for example, on Windows, this equates to invoking
"C:/PROGRA~1/R/R-29~1.1/library/survival/chm/00Index"
on Apple Mac,
"/Library/Frameworks/R.framework/Resources/library/survival/html/00Index.ht=
ml"
etc.)
Details:
---
The help() function returns an object of
class "help_files_with_topic".
The object consists of a character vector
with several attributes.
PC: Windows XP
> library("survival")
> foo <- help("aareg", package =3D "survival")
> class(foo)
[1] "help_files_with_topic"
> foo[1]
[1] "C:/PROGRA~1/R/R-29~1.1/library/survival/chm/aareg"
> attributes(foo)
$call
help(topic =3D "aareg", package =3D "survival")
$pager
[1] "internal"
$topic
[1] "aareg"
$tried_all_packages
[1] FALSE
$type
[1] "chm"
$class
[1] "help_files_with_topic"
> bar <- help("", package =3D "survival")
> class(bar)
[1] "help_files_with_topic"
> bar[1]
[1] NA
> attributes(bar)
$call
help(topic =3D "", package =3D "survival")
$pager
[1] "internal"
$topic
[1] ""
$tried_all_packages
[1] FALSE
$type
[1] "chm"
$class
[1] "help_files_with_topic"
If I alter the character vector to
point to "00Index"
> bar[1] <- "C:/PROGRA~1/R/R-29~1.1/library/survival/chm/00Index"
> bar
I see exactly what I've been attempting to achieve.
Mac OS X:
> foo <- help("aareg", package =3D "survival")
> foo[1]
[1] "/Library/Frameworks/R.framework/Resources/library/survival/html/aareg.=
html"
> attributes(foo)
$call
help(topic =3D "aareg", package =3D "survival")
$pager
[1] "/Library/Frameworks/R.framework/Resources/bin/pager"
$topic
[1] "aareg"
$tried_all_packages
[1] FALSE
$type
[1] "html"
$class
[1] "help_files_with_topic"
> bar <- help("", package =3D "survival")
> bar[1]
[1] NA
> bar[1] <- "/Library/Frameworks/R.framework/Resources/library/survival/htm=
l/00Index.html"
> bar
Again I see exactly what I've been after.
Running R in Emacs on Mac OS X:
> foo <- help(topic =3D "aareg", package =3D "survival")
> foo[1]
[1] "/Library/Frameworks/R.framework/Resources/library/survival/html/aareg.=
html"
> attributes(foo)
$call
help(topic =3D "aareg", package =3D "survival")
$pager
[1] "/Library/Frameworks/R.framework/Resources/bin/pager"
$topic
[1] "aareg"
$tried_all_packages
[1] FALSE
$type
[1] "html"
$class
[1] "help_files_with_topic"
> bar <- help(topic =3D "", package =3D "survival")
> bar[1]
[1] NA
> bar[1] <- "/Library/Frameworks/R.framework/Resources/library/survival/htm=
l/00Index.html"
> bar
Help for '' is shown in browser /usr/bin/open ...
Use
help("", htmlhelp =3D FALSE)
or
options(htmlhelp =3D FALSE)
to revert.
>
Again, what I've been trying to achieve.
When a user loads a new library and doesn't yet know any function names,
I think
> help(package =3D "newLibrary")
or
> ?newLibrary::
should perform the above action whenever possible instead of
producing static help or an error message.
The "00Index" 'object' should be available for such use
whenever it exists. =20
I have not yet worked out all the coding details to make this happen,
but before I do, am I missing some key point? Any reasons why this
would be a Bad Idea?
Steven McKinney, Ph.D.
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: smckinney +at+ bccrc +dot+ ca
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
__
R-devel@r-project.org mailing list
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Re: [Rd] Wishlist: Navigate to "Index" page of help when no topic (PR#13871)
"survival")
> >
> > $pager
> > [1] "/Library/Frameworks/R.framework/Resources/bin/pager"
> >
> > $topic
> > [1] "aareg"
> >
> > $tried_all_packages
> > [1] FALSE
> >
> > $type
> > [1] "html"
> >
> > $class
> > [1] "help_files_with_topic"
> >
> >> bar <- help("", package =3D3D "survival")
> >> bar[1]
> > [1] NA
> >> bar[1] <-
> "/Library/Frameworks/R.framework/Resources/library/survival/htm=3D
> > l/00Index.html"
> >> bar
> >
> > Again I see exactly what I've been after.
> >
> > Running R in Emacs on Mac OS X:
> >
> >> foo <- help(topic =3D3D "aareg", package =3D3D "survival")
> >> foo[1]
> > [1]
> "/Library/Frameworks/R.framework/Resources/library/survival/html/aareg.
> =3D
> > html"
> >> attributes(foo)
> > $call
> > help(topic =3D3D "aareg", package =3D3D "survival")
> >
> > $pager
> > [1] "/Library/Frameworks/R.framework/Resources/bin/pager"
> >
> > $topic
> > [1] "aareg"
> >
> > $tried_all_packages
> > [1] FALSE
> >
> > $type
> > [1] "html"
> >
> > $class
> > [1] "help_files_with_topic"
> >
> >> bar <- help(topic =3D3D "", package =3D3D "survival")
> >> bar[1]
> > [1] NA
> >> bar[1] <-
> "/Library/Frameworks/R.framework/Resources/library/survival/htm=3D
> > l/00Index.html"
> >> bar
> > Help for '' is shown in browser /usr/bin/open ...
> > Use
> > help("", htmlhelp =3D3D FALSE)
> > or
> > options(htmlhelp =3D3D FALSE)
> > to revert.
> >>
> >
> > Again, what I've been trying to achieve.
> >
> > When a user loads a new library and doesn't yet know any function
> names,
> > I think
> >> help(package =3D3D "newLibrary")
> > or
> >> ?newLibrary::
> >
> > should perform the above action whenever possible instead of
> > producing static help or an error message.
> >
> > The "00Index" 'object' should be available for such use
> > whenever it exists. =3D20
> >
> > I have not yet worked out all the coding details to make this happen,
> > but before I do, am I missing some key point? Any reasons why this
> > would be a Bad Idea?
> >
> >
> >
> > Steven McKinney, Ph.D.
> >
> > Statistician
> > Molecular Oncology and Breast Cancer Program
> > British Columbia Cancer Research Centre
> >
> > email: smckinney +at+ bccrc +dot+ ca
> >
> > tel: 604-675-8000 x7561
> >
> > BCCRC
> > Molecular Oncology
> > 675 West 10th Ave, Floor 4
> > Vancouver B.C.
> > V5Z 1L3
> > Canada
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
__
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Re: [Rd] Wishlist: Navigate to "Index" page of help when no topic (PR#13873)
> >>>
> >>> The help() function returns an object of
> >>> class "help_files_with_topic".
> >>> The object consists of a character vector
> >>> with several attributes.
> >>>
> >>> PC: Windows XP
> >>>
> >>>> library("survival")
> >>>> foo <- help("aareg", package =3D3D "survival")
> >>>> class(foo)
> >>> [1] "help_files_with_topic"
> >>>> foo[1]
> >>> [1] "C:/PROGRA~1/R/R-29~1.1/library/survival/chm/aareg"
> >>>> attributes(foo)
> >>> $call
> >>> help(topic =3D3D "aareg", package =3D3D "survival")
> >>>
> >>> $pager
> >>> [1] "internal"
> >>>
> >>> $topic
> >>> [1] "aareg"
> >>>
> >>> $tried_all_packages
> >>> [1] FALSE
> >>>
> >>> $type
> >>> [1] "chm"
> >>>
> >>> $class
> >>> [1] "help_files_with_topic"
> >>>
> >>>> bar <- help("", package =3D3D "survival")
> >>>> class(bar)
> >>> [1] "help_files_with_topic"
> >>>> bar[1]
> >>> [1] NA
> >>>> attributes(bar)
> >>> $call
> >>> help(topic =3D3D "", package =3D3D "survival")
> >>>
> >>> $pager
> >>> [1] "internal"
> >>>
> >>> $topic
> >>> [1] ""
> >>>
> >>> $tried_all_packages
> >>> [1] FALSE
> >>>
> >>> $type
> >>> [1] "chm"
> >>>
> >>> $class
> >>> [1] "help_files_with_topic"
> >>>
> >>> If I alter the character vector to
> >>> point to "00Index"
> >>>
> >>>> bar[1] <- "C:/PROGRA~1/R/R-29~1.1/library/survival/chm/00Index"
> >>>> bar
> >>> I see exactly what I've been attempting to achieve.
> >>>
> >>>
> >>> Mac OS X:
> >>>
> >>>> foo <- help("aareg", package =3D3D "survival")
> >>>> foo[1]
> >>> [1]
> >>
> "/Library/Frameworks/R.framework/Resources/library/survival/html/aareg.
> >> =3D
> >>> html"
> >>>> attributes(foo)
> >>> $call
> >>> help(topic =3D3D "aareg", package =3D3D "survival")
> >>>
> >>> $pager
> >>> [1] "/Library/Frameworks/R.framework/Resources/bin/pager"
> >>>
> >>> $topic
> >>> [1] "aareg"
> >>>
> >>> $tried_all_packages
> >>> [1] FALSE
> >>>
> >>> $type
> >>> [1] "html"
> >>>
> >>> $class
> >>> [1] "help_files_with_topic"
> >>>
> >>>> bar <- help("", package =3D3D "survival")
> >>>> bar[1]
> >>> [1] NA
> >>>> bar[1] <-
> >> "/Library/Frameworks/R.framework/Resources/library/survival/htm=3D
> >>> l/00Index.html"
> >>>> bar
> >>> Again I see exactly what I've been after.
> >>>
> >>> Running R in Emacs on Mac OS X:
> >>>
> >>>> foo <- help(topic =3D3D "aareg", package =3D3D "survival")
> >>>> foo[1]
> >>> [1]
> >>
> "/Library/Frameworks/R.framework/Resources/library/survival/html/aareg.
> >> =3D
> >>> html"
> >>>> attributes(foo)
> >>> $call
> >>> help(topic =3D3D "aareg", package =3D3D "survival")
> >>>
> >>> $pager
> >>> [1] "/Library/Frameworks/R.framework/Resources/bin/pager"
> >>>
> >>> $topic
> >>> [1] "aareg"
> >>>
> >>> $tried_all_packages
> >>> [1] FALSE
> >>>
> >>> $type
> >>> [1] "html"
> >>>
> >>> $class
> >>> [1] "help_files_with_topic"
> >>>
> >>>> bar <- help(topic =3D3D "", package =3D3D "survival")
> >>>> bar[1]
> >>> [1] NA
> >>>> bar[1] <-
> >> "/Library/Frameworks/R.framework/Resources/library/survival/htm=3D
> >>> l/00Index.html"
> >>>> bar
> >>> Help for '' is shown in browser /usr/bin/open ...
> >>> Use
> >>> help("", htmlhelp =3D3D FALSE)
> >>> or
> >>> options(htmlhelp =3D3D FALSE)
> >>> to revert.
> >>> Again, what I've been trying to achieve.
> >>>
> >>> When a user loads a new library and doesn't yet know any function
> >> names,
> >>> I think
> >>>> help(package =3D3D "newLibrary")
> >>> or
> >>>> ?newLibrary::
> >>> should perform the above action whenever possible instead of
> >>> producing static help or an error message.
> >>>
> >>> The "00Index" 'object' should be available for such use
> >>> whenever it exists. =3D20
> >>>
> >>> I have not yet worked out all the coding details to make this
> happen,
> >>> but before I do, am I missing some key point? Any reasons why this
> >>> would be a Bad Idea?
> >>>
> >>>
> >>>
> >>> Steven McKinney, Ph.D.
> >>>
> >>> Statistician
> >>> Molecular Oncology and Breast Cancer Program
> >>> British Columbia Cancer Research Centre
> >>>
> >>> email: smckinney +at+ bccrc +dot+ ca
> >>>
> >>> tel: 604-675-8000 x7561
> >>>
> >>> BCCRC
> >>> Molecular Oncology
> >>> 675 West 10th Ave, Floor 4
> >>> Vancouver B.C.
> >>> V5Z 1L3
> >>> Canada
> >>>
> >>> __
> >>> R-devel@r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >
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Re: [Rd] loadings function (PR#13886)
Hi Mike, Please don't file bug reports without first posing such questions on R-help or R-devel first, asking if such behaviour really is a bug. (This generates extra work for the volunteers who maintain R). In this case, it's your misunderstanding of the information about three different functions on the "loadings" help page. The loadings() function is shown with one argument "x" only. The other parameters described are for the print methods also discussed on the loadings() help page. Looking at the factanal example: > # A little demonstration, v2 is just v1 with noise, > # and same for v4 vs. v3 and v6 vs. v5 > # Last four cases are there to add noise > # and introduce a positive manifold (g factor) > v1 <- c(1,1,1,1,1,1,1,1,1,1,3,3,3,3,3,4,5,6) > v2 <- c(1,2,1,1,1,1,2,1,2,1,3,4,3,3,3,4,6,5) > v3 <- c(3,3,3,3,3,1,1,1,1,1,1,1,1,1,1,5,4,6) > v4 <- c(3,3,4,3,3,1,1,2,1,1,1,1,2,1,1,5,6,4) > v5 <- c(1,1,1,1,1,3,3,3,3,3,1,1,1,1,1,6,4,5) > v6 <- c(1,1,1,2,1,3,3,3,4,3,1,1,1,2,1,6,5,4) > m1 <- cbind(v1,v2,v3,v4,v5,v6) >=20 >=20 > fa <- factanal(m1, factors=3D3) # varimax is the default > fa Call: factanal(x =3D m1, factors =3D 3) Uniquenesses: v1v2v3v4v5v6=20 0.005 0.101 0.005 0.224 0.084 0.005=20 Loadings: Factor1 Factor2 Factor3 v1 0.944 0.182 0.267 =20 v2 0.905 0.235 0.159 =20 v3 0.236 0.210 0.946 =20 v4 0.180 0.242 0.828 =20 v5 0.242 0.881 0.286 =20 v6 0.193 0.959 0.196 =20 Factor1 Factor2 Factor3 SS loadings 1.893 1.886 1.797 Proportion Var 0.316 0.314 0.300 Cumulative Var 0.316 0.630 0.929 The degrees of freedom for the model is 0 and the fit was 0.4755=20 ### Now extract just the loadings > loadings(fa) Loadings: Factor1 Factor2 Factor3 v1 0.944 0.182 0.267 =20 v2 0.905 0.235 0.159 =20 v3 0.236 0.210 0.946 =20 v4 0.180 0.242 0.828 =20 v5 0.242 0.881 0.286 =20 v6 0.193 0.959 0.196 =20 Factor1 Factor2 Factor3 SS loadings 1.893 1.886 1.797 Proportion Var 0.316 0.314 0.300 Cumulative Var 0.316 0.630 0.929 ### Now attempt > loadings(fa, digits =3D 5) Error in loadings(fa, digits =3D 5) : unused argument(s) (digits =3D 5) ### loadings() takes only one argument. ### The digits and other arguments are for the print methods, e.g. > print(fa, digits =3D 5) Call: factanal(x =3D m1, factors =3D 3) Uniquenesses: v1 v2 v3 v4 v5 v6=20 0.00500 0.10090 0.00500 0.22405 0.08429 0.00500=20 Loadings: Factor1 Factor2 Factor3 v1 0.94384 0.18193 0.26661 v2 0.90472 0.23484 0.15948 v3 0.23564 0.20960 0.94634 v4 0.17998 0.24225 0.82757 v5 0.24211 0.88064 0.28560 v6 0.19277 0.95884 0.19621 Factor1 Factor2 Factor3 SS loadings1.89304 1.88576 1.79702 Proportion Var 0.31551 0.31429 0.29950 Cumulative Var 0.31551 0.62980 0.92930 The degrees of freedom for the model is 0 and the fit was 0.4755=20 > print(loadings(fa), digits =3D 5) Loadings: Factor1 Factor2 Factor3 v1 0.94384 0.18193 0.26661 v2 0.90472 0.23484 0.15948 v3 0.23564 0.20960 0.94634 v4 0.17998 0.24225 0.82757 v5 0.24211 0.88064 0.28560 v6 0.19277 0.95884 0.19621 Factor1 Factor2 Factor3 SS loadings1.89304 1.88576 1.79702 Proportion Var 0.31551 0.31429 0.29950 Cumulative Var 0.31551 0.62980 0.92930 >=20 Best Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada From: r-devel-boun...@r-project.org [r-devel-boun...@r-project.org] On Beha= lf Of mikedulr...@gmail.com [mikedulr...@gmail.com] Sent: August 11, 2009 9:15 AM To: r-de...@stat.math.ethz.ch Cc: r-b...@r-project.org Subject: [Rd] loadings function (PR#13886) Full_Name: Mike Ulrich Version: 2.9 OS: Mac OSX Submission from: (NULL) (69.169.178.34) The help documentation for loadings() lists more then one parameter. The function call only expects one parameter. The digits, cutoff, and sort parameters are not used in the function. ## S3 method for class 'loadings': print(x, digits =3D 3, cutoff =3D 0.1, sort =3D FALSE, ...) ## S3 method for class 'factanal': print(x, digits =3D 3, ...) > loadings function (x) x$loadings __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Cannot Change Function (PR#14041)
> -Original Message-
> From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-
> project.org] On Behalf Of Stefan Evert
> Sent: Wednesday, November 04, 2009 4:40 AM
> To: michael_ka...@earthlink.net
> Cc: r-b...@r-project.org; r-de...@stat.math.ethz.ch
> Subject: Re: [Rd] Cannot Change Function (PR#14041)
>=20
> What makes you think this is a bug in R?
>=20
> > Whenever I try changing a function, it keeps coming up with the same
> > error
> > message.
> >
> > I have the function
> > CN_state_log_sum=3Dfunction(Tot_log_sum){ #estimate copy number state
> > for the log
> [...]
> > }
> >
> > When I try to run it in the loop:
> > for (j in 1:length(BB_mean_ref)){ # find copy number states (0 for
> > homozygous
> > deletion, 1 for hemizygous deletion, 2 for neutral, 3 for single
> > amplification,
> > 4 for multiple amplification)
> > state_log_sum[j]=3DCN_state_log_sum(Tot_log_sum[j])
> > state_sum_log[j]=3DCN_state_sum_log(Tot_sum_log[j])
> > }
> > I get the error message:
> > Error in Im(Tot_sum_log) !=3D 0 || Re(Tot_sum_log) <- 2 :
> > could not find function "||<-"
>=20
> The error message indicates that the problem happens in the function
> CN_state_sum_log() rather than CN_state_log_sum(), so it's hardly
> surprising that changing the latter doesn't have any effect.
>=20
> My guess: you've go a condition (Re(Tot_sum_log)<-2), which is
> mistaken for the assignment operator "<-" by the R parser. Adding some
> whitespace (Re(Tot_sum_log) < -2) should help both R and human readers
> to make sense of it.
Adding parentheses around the negative number is the only way to keep
such an expression robustly safe given the various whitespace alterations
that happen as such text passes through different parsers, editors,
mailers, proportional pitch font displays (which can fool human readers) ..=
.
( ( Im(Tot_sum_log) !=3D 0 ) || ( Re(Tot_sum_log) < (-2) ) )
Best
Steven McKinney
>=20
> Best,
> Stefan
>=20
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[Rd] Bug in package stats function ar() (PR#10459)
Full_Name: Steven McKinney Version: 2.6.0 OS: OS X Submission from: (NULL) (142.103.207.10) Function ar() in package "stats" is showing a quirky bug. Some calls to ar() run to completion, others throw an error. The bug is reproducible by several people on different machines, however, the ar() function itself ends up throwing the error sporadically. Several calls to ar() may be necessary to trip the error condition. Code to reproduce: x<-ts(c(-0.2052083,-0.3764986,-0.3762448,0.3740089,0.2737568,2.8235722,-1.7783313,0.2728676,-0.3273164),start=c(1978,3),frequency=4,end=c(1980,3)) # ar function res.ar<-ar(x,aic=TRUE,demean=F) # call "ar" again and res.ar<-ar(x,aic=TRUE,demean=F) Example output: (Note that on this attempt the first call to ar() tripped the error.) > x<-ts(c(-0.2052083,-0.3764986,-0.3762448,0.3740089,0.2737568,2.8235722,- + 1.7783313,0.2728676,-0.3273164),start=c(1978,3),frequency=4,end=c(1980,3)) > > # ar function > res.ar<-ar(x,aic=TRUE,demean=F) Error in if (order > 0) coefs[order, 1:order] else numeric(0) : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In log(var.pred) : NaNs produced 2: In if (order > 0) coefs[order, 1:order] else numeric(0) : the condition has length > 1 and only the first element will be used > > # call "ar" again and > res.ar<-ar(x,aic=TRUE,demean=F) > x Qtr1 Qtr2 Qtr3 Qtr4 1978 -0.2052083 -0.3764986 1979 -0.3762448 0.3740089 0.2737568 2.8235722 1980 -1.7783313 0.2728676 -0.3273164 > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar$resid Qtr1 Qtr2 Qtr3 Qtr4 1978 -0.2052083 -0.3764986 1979 -0.3762448 0.3740089 0.2737568 2.8235722 1980 -1.7783313 0.2728676 -0.3273164 > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar$resid Qtr1 Qtr2 Qtr3 Qtr4 1978 -0.2052083 -0.3764986 1979 -0.3762448 0.3740089 0.2737568 2.8235722 1980 -1.7783313 0.2728676 -0.3273164 > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) Error in if (order > 0) coefs[order, 1:order] else numeric(0) : missing value where TRUE/FALSE needed In addition: Warning message: In if (order > 0) coefs[order, 1:order] else numeric(0) : the condition has length > 1 and only the first element will be used > res.ar<-ar(x,aic=TRUE,demean=F) Error in if (order > 0) coefs[order, 1:order] else numeric(0) : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In log(var.pred) : NaNs produced 2: In if (order > 0) coefs[order, 1:order] else numeric(0) : the condition has length > 1 and only the first element will be used > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > sessionInfo() R version 2.6.0 (2007-10-03) powerpc-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base > ###- Also seen in R 2.5.0: > x<-ts(c(-0.2052083,-0.3764986,-0.3762448,0.3740089,0.2737568,2.8235722,-1.7783313,0.2728676,-0.3273164),start=c(1978,3),frequency=4,end=c(1980,3)) > # ar function > res.ar<-ar(x,aic=TRUE,demean=F) > # call "ar" again and > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) Error in if (order > 0) coefs[order, 1:order] else numeric(0) : missing value where TRUE/FALSE needed In addition: Warning message: the condition has length > 1 and only the first element will be used in: if (order > 0) coefs[order, 1:order] else numeric(0) > sessionInfo() R version 2.5.0 (2007-04-23) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_P APER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" > ###- However, if I lengthen the input vector x<-ts(c(-0.2052083,-0.3764986,-0.3762448,0.3740089,0.2737568,2.8235722,-1.7783313,0.2728676,-0.3273164, -0.2052083,-0.3764986,-0.3762448,0.3740089,0.2737568,2.8235722,-1.7783313,0.2728676,-0.3273164),start=c(1978,3),frequency=4,end=c(1982,3)) I can not trip the error, so perhaps it is due to the short length of the user's input data. ###- Nov 23, 2007 original email from R-help [R] help please Dears Sirs During my computational work
[Rd] lines.formula() problem when data argument is missing (PR#13296)
Full_Name: Steven McKinney
Version: R 2.8.0 Patched svn rev 46845
OS: powerpc-apple-darwin9.5.0
Submission from: (NULL) (142.103.207.10)
<>
lines.formula() throws an error when subset argument is used but nothing is
provided for data argument.
Reproduce:
x<-1:5
y<-c(1,3,NA,2,5)
plot(y~x, type="n") # set up frame
lines(y~x, subset=!is.na(y)) # works OK
lines(y~x, type="o", col="blue") # works OK
# but
lines(y~x, subset=!is.na(y), col="red") # gives an error:
This situation is handled appropriately by points.formula().
Following the coding style of points.formula() the
proposed modifications would be
lines.formula <-
function (formula, data = parent.frame(), ..., subset)
{
m <- match.call(expand.dots = FALSE)
if (is.matrix(eval(m$data, parent.frame(
m$data <- as.data.frame(data)
dots <- m$...
dots <- lapply(dots, eval, data, parent.frame())
m$... <- NULL
m[[1]] <- as.name("model.frame")
m <- as.call(c(as.list(m), list(na.action = NULL)))
mf <- eval(m, parent.frame())
if (!missing(subset)) {
s <- eval(m$subset, data, parent.frame())
###current
### l <- nrow(data)
###\current
###new (as per points.formula)
if (!missing(data)) {
l <- nrow(data)
}
else {
mtmp <- m
mtmp$subset <- NULL
l <- nrow(eval(mtmp, parent.frame()))
}
###\new
dosub <- function(x) if (length(x) == l)
x[s]
else x
###current
###dots <- lapply(dots, dosub, s)
###\current
###new (as per points.formula)
dots <- lapply(dots, dosub)
###\new
}
response <- attr(attr(mf, "terms"), "response")
if (response) {
varnames <- names(mf)
y <- mf[[response]]
if (length(varnames) > 2)
stop("cannot handle more than one 'x' coordinate")
xn <- varnames[-response]
if (length(xn) == 0)
do.call("lines", c(list(y), dots))
else do.call("lines", c(list(mf[[xn]], y), dots))
}
else stop("must have a response variable")
}
Original report from R-help was:
> -Original Message-
> From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
> On Behalf Of John Field
> Sent: Thursday, November 13, 2008 4:41 PM
> To: [EMAIL PROTECTED]
> Subject: [R] lines.formula with subset
>
> Dear list,
>
> When I try to use lines.formula with subset and another argument I
> get an error.
> e.g.
>
> x<-1:5
> y<-c(1,3,NA,2,5)
> plot(y~x, type="n") # set up frame
> lines(y~x, subset=!is.na(y)) # works OK
> lines(y~x, type="o", col="blue") # works OK
> # but
> lines(y~x, subset=!is.na(y), col="red") # gives an error:
>
> Error in if (length(x) == l) x[s] else x : argument is of length zero
>
> Why does this happen?
>
It happens because the function
graphics:::lines.formula
tries to assess the number of rows of data in the data frame
containing the variables in the formula y~x
(see the line of code
l <- nrow(data)
in graphics:::lines.formula
This is the 'el' in the 'length(x) == l'
portion of the line you see in the error message)
Because you did not provide the data frame,
nrow(data) returns NULL, and thus the
if() clause is 'length(x) == NULL' which
yields answer logical(0), an invalid
answer in an if() clause.
Done this way, all is well:
mydf <- data.frame(x = 1:5, y = c(1,3,NA,2,5))
plot(y~x, type="n", data = mydf) # set up frame
lines(y~x, subset=!is.na(y), data = mydf) # works OK
lines(y~x, type="o", col="blue", data = mydf) # works OK
lines(y~x, subset=!is.na(y), col="red", data = mydf) # works OK
The formula - based functions expect to see a dataframe object
from the 'data' arg, but don't enforce this in this case.
This may qualify as a logical bug in the graphics:::lines.formula
function. An error should have been thrown before the if()
clause evaluation, but I'm not sure where in the chain of
function calls the check for a valid data object should be
done and the error thrown. Otherwise, the data objects
y and x that you set up should have been passed downwards
in some fashion for evaluation. R-core members who know
the rules better than I will have to determine how best to
handle this one.
HTH
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: [EMAIL PROTECTED]
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
> With thanks,
> John
>
> =
> John Field Consulting Pty Ltd
> 10 High Street, Burnside SA 5066
> Phone 08 8332 5294 or 0409 097 586
> Fax 08 8332 1229
> Email [EMAIL PROTECTED]
>
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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.
--please do not edit the information
