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Gabor Grothendieck

2004-Jul-26 01:17 UTC

[Rd] directing print.packageInfo to a file

There was a discussion on r-help of getting the output from 
print.packageInfo into a file.  Spencer and I have added a fileargument to
print.packageInfo for consideration in R.  Had this
been available it would have simplified the answer to that
thread.  If the file= argument is used then the packageInfo
information is sent to the file specified rather than displayed
using file.show .

print.packageInfo <- function (x, ..., file = NULL) 
{
    if (!inherits(x, "packageInfo")) 
        stop("wrong class")
    outFile <- if (is.null(file))
	tempfile("RpackageInfo")
    else
	file
    outConn <- file(outFile, open = "w")
    vignetteMsg <- paste("Further information is available in the
following ",
        "vignettes in directory ", sQuote(file.path(x$path,
"doc")),
        ":", sep = "")
    headers <- c("", "Description:\n\n",
"Index:\n\n", paste(paste(strwrap
(vignetteMsg), 
        collapse = "\n"), "\n\n", sep = ""))
    footers <- c("\n", "\n", "\n",
"")
    formatDocEntry <- function(entry) {
        if (is.list(entry) || is.matrix(entry)) 
            formatDL(entry, style = "list")
        else entry
    }
    for (i in which(!sapply(x$info, is.null))) {
        writeLines(headers[i], outConn, sep = "")
        writeLines(formatDocEntry(x$info[[i]]), outConn)
        writeLines(footers[i], outConn, sep = "")
    }
    close(outConn)
    if (is.null(file))
	    file.show(outFile, delete.file = TRUE, title = paste
("Documentation for package", 
		sQuote(x$name)))
    invisible(x)
}

Kurt Hornik

2004-Aug-01 20:56 UTC

head link

[Rd] directing print.packageInfo to a file

>>>>> Gabor Grothendieck writes:
> There was a discussion on r-help of getting the output from 
> print.packageInfo into a file.  Spencer and I have added a file>
argument to print.packageInfo for consideration in R.  Had this
> been available it would have simplified the answer to that
> thread.  If the file= argument is used then the packageInfo
> information is sent to the file specified rather than displayed
> using file.show .
What is wrong with

	capture.output(print.packageInfo(x, ...), file = NULL)

for what you want?

-k
> print.packageInfo <- function (x, ..., file = NULL) 
> {
>     if (!inherits(x, "packageInfo")) 
>         stop("wrong class")
>     outFile <- if (is.null(file))
> 	tempfile("RpackageInfo")
>     else
> 	file
>     outConn <- file(outFile, open = "w")
>     vignetteMsg <- paste("Further information is available in the
following ",
>         "vignettes in directory ", sQuote(file.path(x$path,
"doc")),
>         ":", sep = "")
>     headers <- c("", "Description:\n\n",
"Index:\n\n", paste(paste(strwrap
> (vignetteMsg), 
>         collapse = "\n"), "\n\n", sep = ""))
>     footers <- c("\n", "\n", "\n",
"")
>     formatDocEntry <- function(entry) {
>         if (is.list(entry) || is.matrix(entry)) 
>             formatDL(entry, style = "list")
>         else entry
>     }
>     for (i in which(!sapply(x$info, is.null))) {
>         writeLines(headers[i], outConn, sep = "")
>         writeLines(formatDocEntry(x$info[[i]]), outConn)
>         writeLines(footers[i], outConn, sep = "")
>     }
>     close(outConn)
>     if (is.null(file))
> 	    file.show(outFile, delete.file = TRUE, title = paste
> ("Documentation for package", 
> 		sQuote(x$name)))
>     invisible(x)
> }
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel

Gabor Grothendieck

2004-Aug-01 22:02 UTC

head link

[Rd] directing print.packageInfo to a file

print.packageInfo does not print to the console, it uses file.show.
For example, on R 1.9.1 patched on Windows XP:
> require(chron)
[1] TRUE>  capture.output(print.packageInfo(help(package = chron)), file =
"/abc.txt")
NULL> length(readLines("/abc.txt"))[1] 0


Kurt Hornik <Kurt.Hornik@wu-wien.ac.at> writes:
>>>>> Gabor Grothendieck writes:
> There was a discussion on r-help of getting the output from
> print.packageInfo into a file. Spencer and I have added a file> argument
to print.packageInfo for consideration in R. Had this
> been available it would have simplified the answer to that
> thread. If the file= argument is used then the packageInfo
> information is sent to the file specified rather than displayed
> using file.show .
What is wrong with

     capture.output(print.packageInfo(x, ...), file = NULL)

for what you want?

-k
> print.packageInfo <- function (x, ..., file = NULL)
> {
> if (!inherits(x, "packageInfo"))
> stop("wrong class")
> outFile <- if (is.null(file))
>      tempfile("RpackageInfo")
> else
>      file
> outConn <- file(outFile, open = "w")
> vignetteMsg <- paste("Further information is available in the
following ",
> "vignettes in directory ", sQuote(file.path(x$path,
"doc")),
> ":", sep = "")
> headers <- c("", "Description:\n\n",
"Index:\n\n", paste(paste(strwrap
> (vignetteMsg),
> collapse = "\n"), "\n\n", sep = ""))
> footers <- c("\n", "\n", "\n",
"")
> formatDocEntry <- function(entry) {
> if (is.list(entry) || is.matrix(entry))
> formatDL(entry, style = "list")
> else entry
> }
> for (i in which(!sapply(x$info, is.null))) {
> writeLines(headers[i], outConn, sep = "")
> writeLines(formatDocEntry(x$info[[i]]), outConn)
> writeLines(footers[i], outConn, sep = "")
> }
> close(outConn)
> if (is.null(file))
>       file.show(outFile, delete.file = TRUE, title = paste
> ("Documentation for package",
>           sQuote(x$name)))
> invisible(x)
> }

Kurt Hornik

2004-Aug-02 07:16 UTC

head link

[Rd] directing print.packageInfo to a file

>>>>> Gabor Grothendieck writes:
> 
> print.packageInfo does not print to the console, it uses file.show.
> For example, on R 1.9.1 patched on Windows XP:
> 
>> require(chron)
> [1] TRUE
>> capture.output(print.packageInfo(help(package = chron)), file =
"/abc.txt")
> NULL
>> length(readLines("/abc.txt"))
> [1] 0
But file.show() can be tuned by playing with options(pager).

In your case, something like

  oop <- options(pager = function(file, ...) writeLines(readLines(file)))
  capture.output(print.packageInfo(help(package = "stats")),
	         file = "abc.txt")
  options(oop)

gives

R> length(readLines("abc.txt"))
[1] 345

Hth
-k




> 
> 
> Kurt Hornik <Kurt.Hornik@wu-wien.ac.at> writes:
> 
>>>>> Gabor Grothendieck writes:
> 
>> There was a discussion on r-help of getting the output from
>> print.packageInfo into a file. Spencer and I have added a file>>
argument to print.packageInfo for consideration in R. Had this
>> been available it would have simplified the answer to that
>> thread. If the file= argument is used then the packageInfo
>> information is sent to the file specified rather than displayed
>> using file.show .
> 
> What is wrong with
> 
>      capture.output(print.packageInfo(x, ...), file = NULL)
> 
> for what you want?
> 
> -k
> 
>> print.packageInfo <- function (x, ..., file = NULL)
>> {
>> if (!inherits(x, "packageInfo"))
>> stop("wrong class")
>> outFile <- if (is.null(file))
>> tempfile("RpackageInfo")
>> else
>> file
>> outConn <- file(outFile, open = "w")
>> vignetteMsg <- paste("Further information is available in the
following ",
>> "vignettes in directory ", sQuote(file.path(x$path,
"doc")),
>> ":", sep = "")
>> headers <- c("", "Description:\n\n",
"Index:\n\n", paste(paste(strwrap
>> (vignetteMsg),
>> collapse = "\n"), "\n\n", sep = ""))
>> footers <- c("\n", "\n", "\n",
"")
>> formatDocEntry <- function(entry) {
>> if (is.list(entry) || is.matrix(entry))
>> formatDL(entry, style = "list")
>> else entry
>> }
>> for (i in which(!sapply(x$info, is.null))) {
>> writeLines(headers[i], outConn, sep = "")
>> writeLines(formatDocEntry(x$info[[i]]), outConn)
>> writeLines(footers[i], outConn, sep = "")
>> }
>> close(outConn)
>> if (is.null(file))
>> file.show(outFile, delete.file = TRUE, title = paste
>> ("Documentation for package",
>> sQuote(x$name)))
>> invisible(x)
>> }
> 
> _______________________________________________
> No banners. No pop-ups. No kidding.

Prof Brian Ripley

2004-Aug-02 08:41 UTC

head link

[Rd] directing print.packageInfo to a file

On Mon, 2 Aug 2004, Kurt Hornik wrote:
> >>>>> Gabor Grothendieck writes:
> 
> > 
> > print.packageInfo does not print to the console, it uses file.show.
> > For example, on R 1.9.1 patched on Windows XP:
> > 
> >> require(chron)
> > [1] TRUE
> >> capture.output(print.packageInfo(help(package = chron)), file =
"/abc.txt")
> > NULL
> >> length(readLines("/abc.txt"))
> > [1] 0
> 
> But file.show() can be tuned by playing with options(pager).
> 
> In your case, something like
> 
>   oop <- options(pager = function(file, ...)
writeLines(readLines(file)))
>   capture.output(print.packageInfo(help(package = "stats")),
> 	         file = "abc.txt")
>   options(oop)
> 
> gives
> 
> R> length(readLines("abc.txt"))
> [1] 345
or even

oop <- options(pager="console")

an internal version of the same thing under R for Windows.

-- 
Brian D. Ripley,                  ripley@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, UK                Fax:  +44 1865 272595

Gabor Grothendieck

2004-Aug-02 09:10 UTC

head link

[Rd] directing print.packageInfo to a file

I already suggested using the pager as a workaround
in the original thread although your pager workaround
has the advantage of being 100% in R while mine used
a batch file which defined a new pager.

Note that R already supports

   options(pager = "console")

but if you do this then it seems that capture.output
still won't capture it.  Thus one alternative solution
would be to get capture.output to work with 
pager = "console" and modify print.packageInfo to
take a pager= argument which it would pass down to file.show.
(file.show already has a pager argument.)

Then one could write:

  capture.output( print.packageInfo(help(package = chron), 
            pager = "console"), file = "myfile.txt")

That gets it down to one line although it still seems
unnecessarily indirect when one could just write:

  print.packageInfo(help(package = chron), file = "myfile.txt")

if print.packageInfo just had a file= argument.
Furthermore, print.packageInfo ALREADY creates the file as a 
temporary file to hand over to file.show so its not much of
a stretch to give the user access to what it is already 
creating anyway.

From:   	Kurt Hornik <Kurt.Hornik@wu-wien.ac.at>>>>>> Gabor Grothendieck writes:
>
> print.packageInfo does not print to the console, it uses file.show.
> For example, on R 1.9.1 patched on Windows XP:
>
>> require(chron)
> [1] TRUE
>> capture.output(print.packageInfo(help(package = chron)), file =
"/abc.txt")
> NULL
>> length(readLines("/abc.txt"))
> [1] 0
But file.show() can be tuned by playing with options(pager).

In your case, something like

oop <- options(pager = function(file, ...) writeLines(readLines(file)))
capture.output(print.packageInfo(help(package = "stats")),
      file = "abc.txt")
options(oop)

gives

R> length(readLines("abc.txt"))
[1] 345

Hth
-k




>
>
> Kurt Hornik <Kurt.Hornik@wu-wien.ac.at> writes:
>
>>>>> Gabor Grothendieck writes:
>
>> There was a discussion on r-help of getting the output from
>> print.packageInfo into a file. Spencer and I have added a file>>
argument to print.packageInfo for consideration in R. Had this
>> been available it would have simplified the answer to that
>> thread. If the file= argument is used then the packageInfo
>> information is sent to the file specified rather than displayed
>> using file.show .
>
> What is wrong with
>
> capture.output(print.packageInfo(x, ...), file = NULL)
>
> for what you want?
>
> -k
>
>> print.packageInfo <- function (x, ..., file = NULL)
>> {
>> if (!inherits(x, "packageInfo"))
>> stop("wrong class")
>> outFile <- if (is.null(file))
>> tempfile("RpackageInfo")
>> else
>> file
>> outConn <- file(outFile, open = "w")
>> vignetteMsg <- paste("Further information is available in the
following ",
>> "vignettes in directory ", sQuote(file.path(x$path,
"doc")),
>> ":", sep = "")
>> headers <- c("", "Description:\n\n",
"Index:\n\n", paste(paste(strwrap
>> (vignetteMsg),
>> collapse = "\n"), "\n\n", sep = ""))
>> footers <- c("\n", "\n", "\n",
"")
>> formatDocEntry <- function(entry) {
>> if (is.list(entry) || is.matrix(entry))
>> formatDL(entry, style = "list")
>> else entry
>> }
>> for (i in which(!sapply(x$info, is.null))) {
>> writeLines(headers[i], outConn, sep = "")
>> writeLines(formatDocEntry(x$info[[i]]), outConn)
>> writeLines(footers[i], outConn, sep = "")
>> }
>> close(outConn)
>> if (is.null(file))
>> file.show(outFile, delete.file = TRUE, title = paste
>> ("Documentation for package",
>> sQuote(x$name)))
>> invisible(x)
>> }
>

Gabor Grothendieck

2004-Aug-02 16:07 UTC

head link

[Rd] directing print.packageInfo to a file

From:   	Kurt Hornik <Kurt.Hornik@wu-wien.ac.at>
>>>>> Gabor Grothendieck writes:
>
> I already suggested using the pager as a workaround
> in the original thread although your pager workaround
> has the advantage of being 100% in R while mine used
> a batch file which defined a new pager.
>
> Note that R already supports
>
> options(pager = "console")
>
> but if you do this then it seems that capture.output
> still won't capture it. Thus one alternative solution
> would be to get capture.output to work with
> pager = "console" and modify print.packageInfo to
> take a pager= argument which it would pass down to file.show.
> (file.show already has a pager argument.)
>
> Then one could write:
>
> capture.output( print.packageInfo(help(package = chron),
> pager = "console"), file = "myfile.txt")
>
> That gets it down to one line although it still seems
> unnecessarily indirect when one could just write:
>
> print.packageInfo(help(package = chron), file = "myfile.txt")
>
> if print.packageInfo just had a file= argument.
> Furthermore, print.packageInfo ALREADY creates the file as a
> temporary file to hand over to file.show so its not much of
> a stretch to give the user access to what it is already
> creating anyway.
The point about the proferred solution is that it works generally when
is is desired to capture output that is "printed" via file.show(). If
we start adding extra arguments to print.packageIQR (which is documented
to be internal, btw), we would need to do the same for print.libraryIQR
and print.hsearch and ..., i.e. for all print() methods which in fact
display something using file.show() as a "side effect". That seems
suboptimal to me, when one can wrap the above in a very simple and
generally applicable function (and just calling the print() generic
rather than some method, btw).

---

That's a good point but if a command _already_ produces a file 
I think its logical that access to that file be given directly, 
even if that means having to add a file= argument in many commands.   
In my opinion, both our pager workarounds are too complex/geeky 
for a simple task.

I think this whole thing could be streamlined by extending the
pager= option to accept a connection, e.g.

           options(pager = file("a.txt"))

and then modifying the args of file.show to:

function (..., header = rep("", nfiles), title = "R
Information",
  delete.file = FALSE, file, 
  pager = if (missing(file)) getOption("pager")) else base:file(file))

Now passing down the ... arguments from print.packageInfo
to file.show only involves a one line change, namely, just
add three dots at the end of the call to file.show within
print.packageInfo:

    file.show(outFile, delete.file = TRUE, title = 
        paste("Documentation for package", sQuote(x$name)), ...)

and this automatically gives pager= and file= support to it.
(Note that currently the three dots are already in the arg list to
print.packageInfo but are not used anywhere in the body of that
function.)  Modifying the other functions might be just as easy.

Also, while we are at it we could add pager= arguments
to sink and to capture.output.  With the above any of the following
would work:

   print.packageInfo(help(package = chron), file = "a.txt")

   print.packageInfo(help(package = chron), pager = file("a.txt"))

   capture.output(help(package = chron), pager = file("a.txt"))

   sink(pager = file("a.txt"))
   help(package = chron)
   sink()

   oop <- options(pager = file("a.txt"))
   help(package = chron))
   options(oop)

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