Re: [R] help(package)->sink()
On Sun, 25 Jul 2004, Thomas Lumley wrote:
> On Sat, 24 Jul 2004, Spencer Graves wrote:
>
> >
> > 4. A request for "packageInfo.print" returned "object ... not
> > found".
>
> I think someone may have been contaminated by Java or some such. It should
> be print.packageInfo
>
> > A request for class(mclustInfo) confirmed that it was a
> > packageInfo object, so I tried getMethod("print", "packageInfo"); I
> > got, 'No generic function defined for "print"'. Then I tried,
> > getMethod("show", "packageInfo"); I got, 'No method defined for
> > function "show" and signature object = "packageInfo"'.
> >
>
> For S3 methods you need getS3method("print","packageInfo") rather than
> getMethod.
>
> People often recommend getAnywhere("print.packageInfo"), which does take
> less typing, but I prefer getS3method.
They are not exactly equivalent, though. Although I know of no actual
examples, it is possible to register something like printPackageInfo() as
the S3 method for print() for class "packageInfo". Then getS3method will
work and getAnywhere will not.
The advantage of getAnywhere is that it is blunderbuss designed to pick up
all possible matches for any sort of R object, which can be useful.
--
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: [R] help(package)->sink()
On Sat, 24 Jul 2004, Spencer Graves wrote:
>
> 4. A request for "packageInfo.print" returned "object ... not
> found".
I think someone may have been contaminated by Java or some such. It should
be print.packageInfo
>A request for class(mclustInfo) confirmed that it was a
> packageInfo object, so I tried getMethod("print", "packageInfo"); I
> got, 'No generic function defined for "print"'. Then I tried,
> getMethod("show", "packageInfo"); I got, 'No method defined for
> function "show" and signature object = "packageInfo"'.
>
For S3 methods you need getS3method("print","packageInfo") rather than
getMethod.
People often recommend getAnywhere("print.packageInfo"), which does take
less typing, but I prefer getS3method.
-thomas
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Re: [R] help(package)->sink()
Hi, Gabor:
1. Thanks. I failed to put "mypager.bat" in "/". After I moved
it, I get the following:
> readLines("/mypager.bat")
[1] "type %1 > /mclust.txt"
> old <- options()
> options(pager = "/mypager.bat")
> help(package = "mclust")
> options(old) # reset options back if finished
> head(readLines("/myfile.txt"))
Error in file(con, "r") : unable to open connection
In addition: Warning message:
cannot open file `/myfile.txt'
While R couldn't find the file, it was there, and contained all
the necessary information.
4. Thanks for the tip on print.packageInfo: It worked. [On
other occasions, I've done things like this routinely. I got
sidetracked with the S4 search and frustrated with my failure to get
much out of that, with the result that I failed to see the obvious.]
Vielen Dank noch einmal
spencer graves
Gabor Grothendieck wrote:
Spencer Graves pdf.com> writes:
: 1. I failed to make method 1 work, though I've done that kind of
: thing in the past, and I believe I could make it work if I had to.
:
I am using R 1.9.1 patched on Windows XP and at least there it seems
to work. I did notice that I put a forward slash in the type statement
whereas I meant a backward slash although the forward slash worked anyways,
at least on my system. Here is the output of an R session:
R> readLines("/mypager.bat") # check content of mypager.bat file
[1] "type %1 > /myfile.txt"
R> old <- options()
R> options(pager = "/mypager.bat")
R> help(package = "mclust")
R> options(old) # reset options back if finished
R> head(readLines("/myfile.txt")) # check 1st few lines of myfile.txt
[1] "" " Information on
Package 'mclust'"
[3] "" "Description:"
[5] "" "Package: mclust"
R> R.version.string
[1] "R version 1.9.1, 2004-07-13"
: 4. A request for "packageInfo.print" returned "object ... not
: found". A request for class(mclustInfo) confirmed that it was a
: packageInfo object, so I tried getMethod("print", "packageInfo"); I
: got, 'No generic function defined for "print"'. Then I tried,
: getMethod("show", "packageInfo"); I got, 'No method defined for
: function "show" and signature object = "packageInfo"'.
Sorry about that. I should have written print.packageInfo since
the syntax of these things is genericmethod.class and print is the
generic method and packageInfo is the class.
: Gabor Grothendieck wrote:
:
: >Spencer Graves pdf.com> writes:
: >
: >:
: >: I wanted to direct packageInfo to a file, so I could add comments,
: >: e.g., in MS Word. The following command stored the desired information
: >: in an object:
: >:
: >: mclustInfo <- help(package="mclust")
: >:
: >: Then "mclustInfo" displays it on my screen. To direct it to a
: >: file, I tried the following:
: >:
: >: sink("mclust.txt")
: >: mclustInfo
: >: sink()
: >:
: >: This sequence created an empty file "mclust.txt", while displaying
: >: mclustInfo on my screen. After a few more failed attempts, I gave up
: >: trying to be clever and copied the text from the screen into Word.
: >
: >In addition to your copy and paste solution:
: >
: >1. You could intercept the file.show output by redefining the pager:
: >
: > a. create a one line file called mypager.bat in \ with this line:
: >
: > type %1 > /mclust.txt
: >
: > (with appropriate modifications if you are using UNIX).
: >
: > b. In R issue these commands:
: >
: > old <- options()
: > options(pager = "/mypager.bat")
: > help(package = "mclust")
: > options(old) # reset options back if finished
: >
: >2. Don't use R but go right to the DESCRIPTION and INDEX
: > files. getwd("library/mclust") should show you where
: > to find them.
: >
: >3. If you don't care about the formatting:
: >
: > sink("/mclust.txt")
: > writeLines(unlist(help(package="mclust")$info))
: > sink()
: >
: >4. You could modify packageInfo.print adding a file= argument.
: >
: >__
: >R-help stat.math.ethz.ch mailing list
: >https://www.stat.math.ethz.ch/mailman/listinfo/r-help
: >PLEASE do read the posting guide! http://www.R-project.org/posting-
guide.html
: >
: >
:
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Re: [R] help(package)->sink()
Spencer Graves pdf.com> writes:
: 1. I failed to make method 1 work, though I've done that kind of
: thing in the past, and I believe I could make it work if I had to.
:
I am using R 1.9.1 patched on Windows XP and at least there it seems
to work. I did notice that I put a forward slash in the type statement
whereas I meant a backward slash although the forward slash worked anyways,
at least on my system. Here is the output of an R session:
R> readLines("/mypager.bat") # check content of mypager.bat file
[1] "type %1 > /myfile.txt"
R> old <- options()
R> options(pager = "/mypager.bat")
R> help(package = "mclust")
R> options(old) # reset options back if finished
R> head(readLines("/myfile.txt")) # check 1st few lines of myfile.txt
[1] "" " Information on
Package 'mclust'"
[3] "" "Description:"
[5] "" "Package: mclust"
R> R.version.string
[1] "R version 1.9.1, 2004-07-13"
: 4. A request for "packageInfo.print" returned "object ... not
: found". A request for class(mclustInfo) confirmed that it was a
: packageInfo object, so I tried getMethod("print", "packageInfo"); I
: got, 'No generic function defined for "print"'. Then I tried,
: getMethod("show", "packageInfo"); I got, 'No method defined for
: function "show" and signature object = "packageInfo"'.
Sorry about that. I should have written print.packageInfo since
the syntax of these things is genericmethod.class and print is the
generic method and packageInfo is the class.
: Gabor Grothendieck wrote:
:
: >Spencer Graves pdf.com> writes:
: >
: >:
: >: I wanted to direct packageInfo to a file, so I could add comments,
: >: e.g., in MS Word. The following command stored the desired information
: >: in an object:
: >:
: >: mclustInfo <- help(package="mclust")
: >:
: >: Then "mclustInfo" displays it on my screen. To direct it to a
: >: file, I tried the following:
: >:
: >: sink("mclust.txt")
: >: mclustInfo
: >: sink()
: >:
: >: This sequence created an empty file "mclust.txt", while displaying
: >: mclustInfo on my screen. After a few more failed attempts, I gave up
: >: trying to be clever and copied the text from the screen into Word.
: >
: >In addition to your copy and paste solution:
: >
: >1. You could intercept the file.show output by redefining the pager:
: >
: > a. create a one line file called mypager.bat in \ with this line:
: >
: > type %1 > /mclust.txt
: >
: > (with appropriate modifications if you are using UNIX).
: >
: > b. In R issue these commands:
: >
: > old <- options()
: > options(pager = "/mypager.bat")
: > help(package = "mclust")
: > options(old) # reset options back if finished
: >
: >2. Don't use R but go right to the DESCRIPTION and INDEX
: > files. getwd("library/mclust") should show you where
: > to find them.
: >
: >3. If you don't care about the formatting:
: >
: > sink("/mclust.txt")
: > writeLines(unlist(help(package="mclust")$info))
: > sink()
: >
: >4. You could modify packageInfo.print adding a file= argument.
: >
: >__
: >R-help stat.math.ethz.ch mailing list
: >https://www.stat.math.ethz.ch/mailman/listinfo/r-help
: >PLEASE do read the posting guide! http://www.R-project.org/posting-
guide.html
: >
: >
:
: __
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:
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Re: [R] help(package)->sink()
Thanks to Tom Lumley and Duncan Murdoch for explaining that this
was a feature not a bug and to Gabor Grothendieck for providing several
ways to get around the problem. (Please excuse, Gabor: I should have
said I was using R 1.9.1 under Windows 2000.)
1. I failed to make method 1 work, though I've done that kind of
thing in the past, and I believe I could make it work if I had to.
2. I found the DESCRIPTION and INDEX files. Thanks much. That
not only answers this immediate question, it help me understand how R
packages are structured, which will help me solve many related problems
in the future.
3. Before I sent the email, I tried dump("mclustInfo",
"mclust.txt"). That worked, but I did not like the formatting. I
should have reported that in my email.
4. A request for "packageInfo.print" returned "object ... not
found". A request for class(mclustInfo) confirmed that it was a
packageInfo object, so I tried getMethod("print", "packageInfo"); I
got, 'No generic function defined for "print"'. Then I tried,
getMethod("show", "packageInfo"); I got, 'No method defined for
function "show" and signature object = "packageInfo"'.
Anyway, I now have more than one method that works.
thanks again. spencer graves
Gabor Grothendieck wrote:
Spencer Graves pdf.com> writes:
:
: I wanted to direct packageInfo to a file, so I could add comments,
: e.g., in MS Word. The following command stored the desired information
: in an object:
:
: mclustInfo <- help(package="mclust")
:
: Then "mclustInfo" displays it on my screen. To direct it to a
: file, I tried the following:
:
: sink("mclust.txt")
: mclustInfo
: sink()
:
: This sequence created an empty file "mclust.txt", while displaying
: mclustInfo on my screen. After a few more failed attempts, I gave up
: trying to be clever and copied the text from the screen into Word.
In addition to your copy and paste solution:
1. You could intercept the file.show output by redefining the pager:
a. create a one line file called mypager.bat in \ with this line:
type %1 > /mclust.txt
(with appropriate modifications if you are using UNIX).
b. In R issue these commands:
old <- options()
options(pager = "/mypager.bat")
help(package = "mclust")
options(old) # reset options back if finished
2. Don't use R but go right to the DESCRIPTION and INDEX
files. getwd("library/mclust") should show you where
to find them.
3. If you don't care about the formatting:
sink("/mclust.txt")
writeLines(unlist(help(package="mclust")$info))
sink()
4. You could modify packageInfo.print adding a file= argument.
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Re: [R] help(package)->sink()
Spencer Graves pdf.com> writes:
:
: I wanted to direct packageInfo to a file, so I could add comments,
: e.g., in MS Word. The following command stored the desired information
: in an object:
:
: mclustInfo <- help(package="mclust")
:
: Then "mclustInfo" displays it on my screen. To direct it to a
: file, I tried the following:
:
: sink("mclust.txt")
: mclustInfo
: sink()
:
: This sequence created an empty file "mclust.txt", while displaying
: mclustInfo on my screen. After a few more failed attempts, I gave up
: trying to be clever and copied the text from the screen into Word.
In addition to your copy and paste solution:
1. You could intercept the file.show output by redefining the pager:
a. create a one line file called mypager.bat in \ with this line:
type %1 > /mclust.txt
(with appropriate modifications if you are using UNIX).
b. In R issue these commands:
old <- options()
options(pager = "/mypager.bat")
help(package = "mclust")
options(old) # reset options back if finished
2. Don't use R but go right to the DESCRIPTION and INDEX
files. getwd("library/mclust") should show you where
to find them.
3. If you don't care about the formatting:
sink("/mclust.txt")
writeLines(unlist(help(package="mclust")$info))
sink()
4. You could modify packageInfo.print adding a file= argument.
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Re: [R] help(package)->sink()
On Sat, 24 Jul 2004 10:06:02 -0700, Spencer Graves
<[EMAIL PROTECTED]> wrote:
> I wanted to direct packageInfo to a file, so I could add comments,
>e.g., in MS Word. The following command stored the desired information
>in an object:
>
> mclustInfo <- help(package="mclust")
>
> Then "mclustInfo" displays it on my screen. To direct it to a
>file, I tried the following:
>
> sink("mclust.txt")
> mclustInfo
> sink()
>
> This sequence created an empty file "mclust.txt", while displaying
>mclustInfo on my screen. After a few more failed attempts, I gave up
>trying to be clever and copied the text from the screen into Word.
>
> Is this a bug, that sink does not capture the output of objects of
>class packageInfo?
I don't think so. The print method for that class calls other code to
display it; it doesn't go through the regular "display to console"
route. Instead, it writes the help page to a file, then calls
file.show.
It's possible that on some systems file.show would just dump the file
to the console, but that's not what happens on Windows, for example.
Duncan Murdoch
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Re: [R] help(package)->sink()
On Sat, 24 Jul 2004, Spencer Graves wrote:
> I wanted to direct packageInfo to a file, so I could add comments,
> e.g., in MS Word. The following command stored the desired information
> in an object:
>
> mclustInfo <- help(package="mclust")
>
> Then "mclustInfo" displays it on my screen. To direct it to a
> file, I tried the following:
>
> sink("mclust.txt")
> mclustInfo
> sink()
>
> This sequence created an empty file "mclust.txt", while displaying
> mclustInfo on my screen. After a few more failed attempts, I gave up
> trying to be clever and copied the text from the screen into Word.
>
> Is this a bug, that sink does not capture the output of objects of
> class packageInfo?
>
Not really. The output doesn't really appear on your screen, it appears
on your pager. In your case the pager is the screen, so this isn't
obvious.
-thomas
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[R] help(package)->sink()
I wanted to direct packageInfo to a file, so I could add comments,
e.g., in MS Word. The following command stored the desired information
in an object:
mclustInfo <- help(package="mclust")
Then "mclustInfo" displays it on my screen. To direct it to a
file, I tried the following:
sink("mclust.txt")
mclustInfo
sink()
This sequence created an empty file "mclust.txt", while displaying
mclustInfo on my screen. After a few more failed attempts, I gave up
trying to be clever and copied the text from the screen into Word.
Is this a bug, that sink does not capture the output of objects of
class packageInfo?
Best Wishes,
spencer graves
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