Re: [Rd] html help fails for named vector objects (PR#9927)
[EMAIL PROTECTED] wrote:
>help(letters, htmlhelp=TRUE) fails.
>
> Under the Mac OSX gui, the message is 'Help for the topic "a" was not
> found.' Under the version documented below, and under Windows, the
> message is
>
>"No documentation for 'a' in specified packages and libraries:"
> repeated for all the elements of letters, then followed by
>"you could try 'help.search("a")'",
> again repeated for all elements of letters.
>
> The outcome seems similar for any character vector (including matrix)
> object, e.g. the matrix 'primateDNA' in the DAAGbio package.
>
> The following have the expected result
>help("letters", htmlhelp=TRUE)
>help(letters, htmlhelp=FALSE)
>
>
Not for me. I get the same thing with or without htmlhelp. (That IS what
I expected, though)
The logic in help is
ischar <- try(is.character(topic), silent = TRUE)
if (inherits(ischar, "try-error"))
ischar <- FALSE
if (!ischar)
topic <- deparse(substitute(topic))
So a character argument implies that it contains the names of help
topics. That isn't quite what the documentation says, though:
topic: usually, the name on which documentation is sought. The name
may be quoted or unquoted (but note that if 'topic' is the
name of a variable containing a character string
documentation is provided for the name, not for the character
string).
It is the documentation that is wrong. We could implement what it says,
but then it would be a require considerable contortions to get help on a
topic stored in a variable (e.g., coming from a help field in a GUI).
It isn't clear to me that it should try all elements of a character
vector of length > 1. That looks like a bit of a booby trap to me --
what if it accidentally caught a variable with a few million elements? A
length check should be rather easy.
> The same result is obtained with R-2.5.1.
>
>
> --please do not edit the information below--
>
> Version:
> platform = i386-apple-darwin8.10.1
> arch = i386
> os = darwin8.10.1
> system = i386, darwin8.10.1
> status = beta
> major = 2
> minor = 6.0
> year = 2007
> month = 09
> day = 22
> svn rev = 42941
> language = R
> version.string = R version 2.6.0 beta (2007-09-22 r42941)
>
> Locale:
> C
>
> Search Path:
> .GlobalEnv, package:testpkg, package:stats, package:graphics,
> package:grDevices, package:utils, package:datasets, package:methods,
> Autoloads, package:base
>
> John Maindonald email: [EMAIL PROTECTED]
> phone : +61 2 (6125)3473fax : +61 2(6125)5549
> Centre for Mathematics & Its Applications, Room 1194,
> John Dedman Mathematical Sciences Building (Building 27)
> Australian National University, Canberra ACT 0200.
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
--
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
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [Rd] html help fails for named vector objects (PR#9927)
On a normal R help system any version of help(letters) tries to give you
help on a, b, etc. This is intentional (although the documentation is
unclearly worded), and has been the case since at least R 2.0.0.
Some versions of help will display only the first topic.
If help(letters, htmlhelp=FALSE) does something else on your system, that
is a MacOS-specific bug since the topic selected should not depend on the
optional arguments.
What is unclear from the documentation is what should happen with
help(c("help", "help.search"))
It seems that for text help you get the first, for htmlhelp both.
There are two things we could do to help (apart from clarifying the
documentation):
1) If 'topic' is neither a name nor a character vector (e.g. an expression
like the last example) give an explicit error.
2) if topic is a character vector of length > 1, use the name.
On Sun, 23 Sep 2007, [EMAIL PROTECTED] wrote:
> help(letters, htmlhelp=TRUE) fails.
>
> Under the Mac OSX gui, the message is 'Help for the topic "a" was not
> found.' Under the version documented below, and under Windows, the
> message is
>
> "No documentation for 'a' in specified packages and libraries:"
> repeated for all the elements of letters, then followed by
> "you could try 'help.search("a")'",
> again repeated for all elements of letters.
>
> The outcome seems similar for any character vector (including matrix)
> object, e.g. the matrix 'primateDNA' in the DAAGbio package.
>
> The following have the expected result
> help("letters", htmlhelp=TRUE)
> help(letters, htmlhelp=FALSE)
But the documented and actual results are the same, and different in the
two cases.
> The same result is obtained with R-2.5.1.
>
>
> --please do not edit the information below--
>
> Version:
> platform = i386-apple-darwin8.10.1
> arch = i386
> os = darwin8.10.1
> system = i386, darwin8.10.1
> status = beta
> major = 2
> minor = 6.0
> year = 2007
> month = 09
> day = 22
> svn rev = 42941
> language = R
> version.string = R version 2.6.0 beta (2007-09-22 r42941)
>
> Locale:
> C
>
> Search Path:
> .GlobalEnv, package:testpkg, package:stats, package:graphics,
> package:grDevices, package:utils, package:datasets, package:methods,
> Autoloads, package:base
>
> John Maindonald email: [EMAIL PROTECTED]
> phone : +61 2 (6125)3473fax : +61 2(6125)5549
> Centre for Mathematics & Its Applications, Room 1194,
> John Dedman Mathematical Sciences Building (Building 27)
> Australian National University, Canberra ACT 0200.
>
> __
> R-devel@r-project.org 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] html help fails for named vector objects (PR#9927)
On a normal R help system any version of help(letters) tries to give you
help on a, b, etc. This is intentional (although the documentation is
unclearly worded), and has been the case since at least R 2.0.0.
Some versions of help will display only the first topic.
If help(letters, htmlhelp=FALSE) does something else on your system, that
is a MacOS-specific bug since the topic selected should not depend on the
optional arguments.
What is unclear from the documentation is what should happen with
help(c("help", "help.search"))
It seems that for text help you get the first, for htmlhelp both.
There are two things we could do to help (apart from clarifying the
documentation):
1) If 'topic' is neither a name nor a character vector (e.g. an expression
like the last example) give an explicit error.
2) if topic is a character vector of length > 1, use the name.
On Sun, 23 Sep 2007, [EMAIL PROTECTED] wrote:
> help(letters, htmlhelp=TRUE) fails.
>
> Under the Mac OSX gui, the message is 'Help for the topic "a" was not
> found.' Under the version documented below, and under Windows, the
> message is
>
> "No documentation for 'a' in specified packages and libraries:"
> repeated for all the elements of letters, then followed by
> "you could try 'help.search("a")'",
> again repeated for all elements of letters.
>
> The outcome seems similar for any character vector (including matrix)
> object, e.g. the matrix 'primateDNA' in the DAAGbio package.
>
> The following have the expected result
> help("letters", htmlhelp=TRUE)
> help(letters, htmlhelp=FALSE)
But the documented and actual results are the same, and different in the
two cases.
> The same result is obtained with R-2.5.1.
>
>
> --please do not edit the information below--
>
> Version:
> platform = i386-apple-darwin8.10.1
> arch = i386
> os = darwin8.10.1
> system = i386, darwin8.10.1
> status = beta
> major = 2
> minor = 6.0
> year = 2007
> month = 09
> day = 22
> svn rev = 42941
> language = R
> version.string = R version 2.6.0 beta (2007-09-22 r42941)
>
> Locale:
> C
>
> Search Path:
> .GlobalEnv, package:testpkg, package:stats, package:graphics,
> package:grDevices, package:utils, package:datasets, package:methods,
> Autoloads, package:base
>
> John Maindonald email: [EMAIL PROTECTED]
> phone : +61 2 (6125)3473fax : +61 2(6125)5549
> Centre for Mathematics & Its Applications, Room 1194,
> John Dedman Mathematical Sciences Building (Building 27)
> Australian National University, Canberra ACT 0200.
>
> __
> R-devel@r-project.org 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] html help fails for named vector objects (PR#9927)
There seems also to be a difference between the way 'help()' and '?'
handle 'topic' in some cases.
Consider:
lm <- "aov"
The following all bring up help for 'lm':
?lm
?"lm"
help("lm")
This opens help for 'aov':
help(lm)
It seems that "?" doesn't care about quoting, but "help" does.
Did I miss something in the docs?
(If it matters, I'm using options(chmhelp=TRUE).)
> sessionInfo()
R version 2.6.0 beta (2007-09-18 r42895)
i386-pc-mingw32
locale:
LC_COLLATE=English_Canada.1252; [snip]
attached base packages:
[1] stats graphics grDevices utils datasets methods base
- Peter Ehlers
Prof Brian Ripley wrote:
> On a normal R help system any version of help(letters) tries to give you
> help on a, b, etc. This is intentional (although the documentation is
> unclearly worded), and has been the case since at least R 2.0.0.
> Some versions of help will display only the first topic.
>
> If help(letters, htmlhelp=FALSE) does something else on your system, that
> is a MacOS-specific bug since the topic selected should not depend on the
> optional arguments.
>
> What is unclear from the documentation is what should happen with
>
> help(c("help", "help.search"))
>
> It seems that for text help you get the first, for htmlhelp both.
>
> There are two things we could do to help (apart from clarifying the
> documentation):
>
> 1) If 'topic' is neither a name nor a character vector (e.g. an expression
> like the last example) give an explicit error.
>
> 2) if topic is a character vector of length > 1, use the name.
>
>
> On Sun, 23 Sep 2007, [EMAIL PROTECTED] wrote:
>
>> help(letters, htmlhelp=TRUE) fails.
>>
>> Under the Mac OSX gui, the message is 'Help for the topic "a" was not
>> found.' Under the version documented below, and under Windows, the
>> message is
>>
>> "No documentation for 'a' in specified packages and libraries:"
>> repeated for all the elements of letters, then followed by
>> "you could try 'help.search("a")'",
>> again repeated for all elements of letters.
>>
>> The outcome seems similar for any character vector (including matrix)
>> object, e.g. the matrix 'primateDNA' in the DAAGbio package.
>>
>> The following have the expected result
>> help("letters", htmlhelp=TRUE)
>> help(letters, htmlhelp=FALSE)
>
> But the documented and actual results are the same, and different in the
> two cases.
>
>> The same result is obtained with R-2.5.1.
>>
>>
>> --please do not edit the information below--
>>
>> Version:
>> platform = i386-apple-darwin8.10.1
>> arch = i386
>> os = darwin8.10.1
>> system = i386, darwin8.10.1
>> status = beta
>> major = 2
>> minor = 6.0
>> year = 2007
>> month = 09
>> day = 22
>> svn rev = 42941
>> language = R
>> version.string = R version 2.6.0 beta (2007-09-22 r42941)
>>
>> Locale:
>> C
>>
>> Search Path:
>> .GlobalEnv, package:testpkg, package:stats, package:graphics,
>> package:grDevices, package:utils, package:datasets, package:methods,
>> Autoloads, package:base
>>
>> John Maindonald email: [EMAIL PROTECTED]
>> phone : +61 2 (6125)3473fax : +61 2(6125)5549
>> Centre for Mathematics & Its Applications, Room 1194,
>> John Dedman Mathematical Sciences Building (Building 27)
>> Australian National University, Canberra ACT 0200.
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
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[Rd] initial scrambling of seed in do_setseed / RNG_Init
I would like to suggest a modification of initial scrambling of the
seed in RNG_Init (called from do_setseed). The modified code is
equivalent, but faster. Patch against R-devel_2007-09-22 follows
--- R-devel-orig/src/main/RNG.c 2007-09-02 07:49:35.0 +0200
+++ R-devel-modif/src/main/RNG.c2007-09-23 10:51:59.234566440 +0200
@@ -216,8 +216,8 @@
BM_norm_keep = 0.0; /* zap Box-Muller history */
/* Initial scrambling */
-for(j = 0; j < 50; j++)
- seed = (69069 * seed + 1);
+/* Equivalent to 50 iterations of seed = (69069 * seed + 1) */
+seed = (1100682473U * seed + 2358491998U);
switch(kind) {
case WICHMANN_HILL:
case MARSAGLIA_MULTICARRY:
Let me add also the following remark. The help(Random.user) page says
Optionally, the user can supply the entry point 'user_unif_init',
which is called with an 'unsigned int' argument when 'RNGkind' (or
'set.seed') is called, and is intended to be used to initialize
the user's RNG code. The argument is intended to be used to set
the "seeds"; it is the 'seed' argument to 'set.seed' or an
essentially random seed if 'RNGkind' is called.
I want to comment on the sentence
The argument is intended to be used to set
the "seeds"; it is the 'seed' argument to 'set.seed' or
This is not correct. If user_unif_init is called from set.seed, then
it receives the argument of set.seed after the initial scrambling.
If someone writes a user defined generator and wishes to get the original
seed specified in set.seed (which is my situation), then it may be useful
for him to know that the transformation
seed = 3602842457U * (seed - 2358491998U);
is the inverse to the initial scrambling. Hence, if it is applied to the
value received by user_unif_init, it provides the original value specified
by the user in set.seed.
Let me point out that the initial scrambling does not eliminate seed 0.
It only decreases the probability that this seed is sent to the generator.
Due to scrambling, the entry point user_unif_init receives 0 not as a
consequence of set.seed(0), but as a consequence of set.seed(105890386).
This is less likely, but still possible.
I suggest to clarify the page help(Random.user) concerning the transformation
of the seed. For example, the sentence
it is the 'seed' argument to 'set.seed'
may be extended to
it is the 'seed' argument to 'set.seed' after a transformation described
in function RNG_Init in src/main/RNG.c
Also, a remark concerning the inverse transformation may be add. In my opinion,
the best way to do this could be to add a comment to RNG_Init in src/main/RNG.c,
saying, for example:
If you need to undo the initial scrambling in user_unif_init, use
seed = 3602842457U * (seed - 2358491998U);
Petr Savicky.
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Re: [Rd] html help fails for named vector objects (PR#9927)
On Sun, 23 Sep 2007, P Ehlers wrote:
> There seems also to be a difference between the way 'help()' and '?'
> handle 'topic' in some cases.
Yes, that is intentional. I didn't mention it (after deliberation) as the
bug report was about help(htmlhelp=TRUE) and not ?. I did mention
clarifying the documentation, which in my draft says
topic: usually, a name or character string specifying the topic for
which help is sought.
For 'help', if 'topic' is a length-one character vector, the
topic is taken to be the value of the only element.
For '?' the 'topic' argument may also be a function call, to
ask for documentation on a corresponding method. See the
section on S4 method documentation.
but I am still tweaking.
> Consider:
> lm <- "aov"
>
> The following all bring up help for 'lm':
> ?lm
> ?"lm"
> help("lm")
>
> This opens help for 'aov':
> help(lm)
>
> It seems that "?" doesn't care about quoting, but "help" does.
> Did I miss something in the docs?
No, as it is not in the docs as yet. The help page described what happens
for ?, not for help, e.g.
The 'topic' argument may also be a function call, to ask for
documentation on a corresponding method. See the section on
method documentation.
applies only to ? .
> (If it matters, I'm using options(chmhelp=TRUE).)
It will not if utils::help is being called.
>
>> sessionInfo()
> R version 2.6.0 beta (2007-09-18 r42895)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_Canada.1252; [snip]
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> - Peter Ehlers
>
> Prof Brian Ripley wrote:
>> On a normal R help system any version of help(letters) tries to give you
>> help on a, b, etc. This is intentional (although the documentation is
>> unclearly worded), and has been the case since at least R 2.0.0.
>> Some versions of help will display only the first topic.
>>
>> If help(letters, htmlhelp=FALSE) does something else on your system, that
>> is a MacOS-specific bug since the topic selected should not depend on the
>> optional arguments.
>>
>> What is unclear from the documentation is what should happen with
>>
>> help(c("help", "help.search"))
>>
>> It seems that for text help you get the first, for htmlhelp both.
>>
>> There are two things we could do to help (apart from clarifying the
>> documentation):
>>
>> 1) If 'topic' is neither a name nor a character vector (e.g. an expression
>> like the last example) give an explicit error.
>>
>> 2) if topic is a character vector of length > 1, use the name.
>>
>>
>> On Sun, 23 Sep 2007, [EMAIL PROTECTED] wrote:
>>
>>> help(letters, htmlhelp=TRUE) fails.
>>>
>>> Under the Mac OSX gui, the message is 'Help for the topic "a" was not
>>> found.' Under the version documented below, and under Windows, the
>>> message is
>>>
>>> "No documentation for 'a' in specified packages and libraries:"
>>> repeated for all the elements of letters, then followed by
>>> "you could try 'help.search("a")'",
>>> again repeated for all elements of letters.
>>>
>>> The outcome seems similar for any character vector (including matrix)
>>> object, e.g. the matrix 'primateDNA' in the DAAGbio package.
>>>
>>> The following have the expected result
>>> help("letters", htmlhelp=TRUE)
>>> help(letters, htmlhelp=FALSE)
>>
>> But the documented and actual results are the same, and different in the
>> two cases.
>>
>>> The same result is obtained with R-2.5.1.
>>>
>>>
>>> --please do not edit the information below--
>>>
>>> Version:
>>> platform = i386-apple-darwin8.10.1
>>> arch = i386
>>> os = darwin8.10.1
>>> system = i386, darwin8.10.1
>>> status = beta
>>> major = 2
>>> minor = 6.0
>>> year = 2007
>>> month = 09
>>> day = 22
>>> svn rev = 42941
>>> language = R
>>> version.string = R version 2.6.0 beta (2007-09-22 r42941)
>>>
>>> Locale:
>>> C
>>>
>>> Search Path:
>>> .GlobalEnv, package:testpkg, package:stats, package:graphics,
>>> package:grDevices, package:utils, package:datasets, package:methods,
>>> Autoloads, package:base
>>>
>>> John Maindonald email: [EMAIL PROTECTED]
>>> phone : +61 2 (6125)3473fax : +61 2(6125)5549
>>> Centre for Mathematics & Its Applications, Room 1194,
>>> John Dedman Mathematical Sciences Building (Building 27)
>>> Australian National University, Canberra ACT 0200.
>>>
>>> __
>>> R-devel@r-project.org 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
__
R-devel@r-project.org mailing list
htt
[Rd] Inspecting promises
Is there some way of displaying the expression and evaluation environment
associated with a promise? I have found the following:
> # first run these two commands to set up example
> e <- new.env()
> delayedAssign("y", x*x, assign.env = e)
> # method 1. shows expression but not evaluation environment
> str(as.list(e))
List of 1
$ y: promise to language x * x
> # method 2. shows expression but not evaluation environment
> substitute(y, e)
x * x
which shows two different ways of displaying the expression
associated with a promise but neither shows the evaluation
environment. The first technique may actually be a bug in
R based on previous discussion on r-devel.
Is there a way to display both the expression and the evaluation
environment associated with a promise. Its a bit difficult to debug
code involving promises if you can't inspect the objects you are
working with.
> R.version.string # Vista
[1] "R version 2.6.0 beta (2007-09-19 r42914)"
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