Hi,
1-
How is it possible to use the name of a generic function as
the name of a function which is not related to the generic
function? For example, if I define predict.my.function, R
will relate it to predict function and I'll get the following
warning when I run R CMD check
* checking S3 generic/method consistency ... WARNING
predict:
? function(object, ...)
predict.my.function ...
2- I get the following warning although I have used "require" of the related library in the function and imports in DESCRIPTION file
no visible global function definition for coxph
3- Although I use the alias of an Rd file of my package in cross references:
\seealso{
See Also as \code{\link{object.name}}
}
where object.name is the name of an Rd file without Rd, I get the following warning
Missing link(s) in documentation object './man/object.name.Rd':
object.name
I don't think that I will have use the name of my package.
Look forward to your reply,
Carol
some problems reported in 00check.log
12 messages · carol white, Uwe Ligges, Brian Ripley
On 17.09.2010 14:25, carol white wrote:
Hi, 1- How is it possible to use the name of a generic function as the name of a function which is not related to the generic function?
This is not possible, choose a different name or make it a predict() methods. > For example, if I define predict.my.function, R
will relate it to predict function and I'll get the following
warning when I run R CMD check
* checking S3 generic/method consistency ... WARNING
predict:
function(object, ...)
predict.my.function ...
2- I get the following warning although I have used "require" of the related library in the function and imports in DESCRIPTION file no visible global function definition for coxph
If you do not import it into your namespace but make it available via require() instead, you need to declare it as Depends.
3- Although I use the alias of an Rd file of my package in cross references:
\seealso{
See Also as \code{\link{object.name}}
}
where object.name is the name of an Rd file without Rd
What is "an Rd file without Rd"?
, I get the following warning Missing link(s) in documentation object './man/object.name.Rd': object.name
This means you cited the help page itself? I think you need to tell us the alias(es) you used as well as the purpose of this one.
I don't think that I will have use the name of my package.
Why is this related? Best wishes, Uwe Ligges
Look forward to your reply, Carol
______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Thank you for your reply.
--- On Fri, 9/17/10, Uwe Ligges <ligges at statistik.tu-dortmund.de> wrote:
From: Uwe Ligges <ligges at statistik.tu-dortmund.de> Subject: Re: [Rd] some problems reported in 00check.log To: "carol white" <wht_crl at yahoo.com> Cc: r-devel at r-project.org Date: Friday, September 17, 2010, 10:45 AM
regarding the point 3,
Suppose I have a data set, data.set1 with data.set1.Rd and data.set2 with data.set2.Rd that are related to each other. then, I put in \seealso field
in data.set2.Rd
\seealso{
See Also as \code{\link{data.set1}}
and in data.set1.Rd
\seealso{
See Also as \code{\link{data.set2}}
But I get the aforementioned warning that I don't understand why.
Missing link(s) in documentation object
'./man/object.name.Rd':
object.name
There is another problem. I have installed two packages in another path than the library path of R. how could I load them for R CMD check (where to indicate the path for lib.loc) as I get error message due to require of these two packages in different functions?
3- Although I use the alias of an Rd file of my
package in cross references:
\seealso{
See Also as \code{\link{object.name}}
}
where object.name is the name of an Rd file without
Rd What is "an Rd file without Rd"?
, I get the following warning Missing link(s) in documentation object
'./man/object.name.Rd':
object.name
This means you cited the help page itself? I think you need to tell us the alias(es) you used as well as the purpose of this one.
???I don't think that I will have use
the name of my package. Why is this related? Best wishes, Uwe Ligges
Look forward to your reply, ???Carol
______________________________________________ R-devel at r-project.org
mailing list
On 17.09.2010 20:15, carol white wrote:
Thank you for your reply. --- On Fri, 9/17/10, Uwe Ligges<ligges at statistik.tu-dortmund.de> wrote:
From: Uwe Ligges<ligges at statistik.tu-dortmund.de> Subject: Re: [Rd] some problems reported in 00check.log To: "carol white"<wht_crl at yahoo.com> Cc: r-devel at r-project.org Date: Friday, September 17, 2010, 10:45 AM
regarding the point 3,
Suppose I have a data set, data.set1 with data.set1.Rd and data.set2 with data.set2.Rd that are related to each other. then, I put in \seealso field
in data.set2.Rd
\seealso{
See Also as \code{\link{data.set1}}
and in data.set1.Rd
\seealso{
See Also as \code{\link{data.set2}}
But I get the aforementioned warning that I don't understand why.
Missing link(s) in documentation object
'./man/object.name.Rd':
object.name
In that case I guess you forgot to specify the aliases appropriately?
There is another problem. I have installed two packages in another path than the library path of R. how could I load them for R CMD check (where to indicate the path for lib.loc) as I get error message due to require of these two packages in different functions?
For example, specify all relevant libraries in the environment variable R_LIBS. Best, Uwe Ligges
3- Although I use the alias of an Rd file of my
package in cross references:
\seealso{
See Also as \code{\link{object.name}}
}
where object.name is the name of an Rd file without
Rd What is "an Rd file without Rd"?
, I get the following warning Missing link(s) in documentation object
'./man/object.name.Rd':
object.name
This means you cited the help page itself? I think you need to tell us the alias(es) you used as well as the purpose of this one.
I don't think that I will have use
the name of my package. Why is this related? Best wishes, Uwe Ligges
Look forward to your reply,
Carol
______________________________________________ R-devel at r-project.org
mailing list
3 days later
Thank you very much Uwe. It works now. I have a question about pdf formating in pdf manual file: How to format the long lines which go to the margin? For ex, this happens in Usage field if a function has many arguments. Also, it happens in examples or Arugment sections when the lines are long. Best, Carol
On Wed, 22 Sep 2010, carol white wrote:
Thank you very much Uwe. It works now. I have a question about pdf formating in pdf manual file: How to format the long lines which go to the margin? For ex, this happens in Usage field if a function has many arguments. Also, it happens in examples or Arugment sections when the lines are long.
Correct the sources by re-formatting over-long lines yourself. (This
should only happen in verbatim-like sections, hence unlikely to happen
in \argument{}.)
One of the things we suggest when checking a package is to read
through the PDF manual, and this is one of the problems to look out
for. (Note that it does depend on the fonts used for the PDF, but the
default Courier for monospaced text is somewhat wide.)
Brian D. Ripley, ripley at 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
So there is no sort of automatic way like using a markup command for the susceptible fields instead of splitting manually a line on different lines? True that this doesn't happen in Arguments field (I confused with Format field). Also true that the codes used in Usage, Examples etc are in courrier. Is there any way to reduce the size and not to change the font of character for these fields? Best, Carol
--- On Wed, 9/22/10, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
From: Prof Brian Ripley <ripley at stats.ox.ac.uk> Subject: Re: [Rd] some problems reported in 00check.log To: "carol white" <wht_crl at yahoo.com> Cc: "Uwe Ligges" <ligges at statistik.tu-dortmund.de>, r-devel at r-project.org Date: Wednesday, September 22, 2010, 2:15 AM On Wed, 22 Sep 2010, carol white wrote:
Thank you very much Uwe. It works now. I have a question about pdf formating in pdf manual
file:
How to format the long lines which go to the margin?
For ex, this happens in Usage field if a function has many
arguments. Also, it happens in examples or Arugment sections
when the lines are long.
Correct the sources by re-formatting over-long lines
yourself.? (This should only happen in verbatim-like
sections, hence unlikely to happen in \argument{}.)
One of the things we suggest when checking a package is to
read through the PDF manual, and this is one of the problems
to look out for.? (Note that it does depend on the
fonts used for the PDF, but the default Courier for
monospaced text is somewhat wide.)
-- Brian D. Ripley,? ? ? ? ?
? ? ? ? ripley at 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
On Wed, 22 Sep 2010, carol white wrote:
So there is no sort of automatic way like using a markup command for the susceptible fields instead of splitting manually a line on different lines?
Well, how is the automatic command to know how to do this? As you will see from the autmatic wrapping in e.g. deparse(), we are not able to do a very good job. There has been some talk about doing this automatically as a backstop, but I don't know the current state: in any case it does not happen in released versions of R.
True that this doesn't happen in Arguments field (I confused with Format field). Also true that the codes used in Usage, Examples etc are in courrier. Is there any way to reduce the size and not to change the font of character for these fields?
You can change Rd.sty, which already contains options for using other fontsets.
Best, Carol --- On Wed, 9/22/10, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
From: Prof Brian Ripley <ripley at stats.ox.ac.uk> Subject: Re: [Rd] some problems reported in 00check.log To: "carol white" <wht_crl at yahoo.com> Cc: "Uwe Ligges" <ligges at statistik.tu-dortmund.de>, r-devel at r-project.org Date: Wednesday, September 22, 2010, 2:15 AM On Wed, 22 Sep 2010, carol white wrote:
Thank you very much Uwe. It works now. I have a question about pdf formating in pdf manual
file:
How to format the long lines which go to the margin?
For ex, this happens in Usage field if a function has many
arguments. Also, it happens in examples or Arugment sections
when the lines are long.
Correct the sources by re-formatting over-long lines
yourself.? (This should only happen in verbatim-like
sections, hence unlikely to happen in \argument{}.)
One of the things we suggest when checking a package is to
read through the PDF manual, and this is one of the problems
to look out for.? (Note that it does depend on the
fonts used for the PDF, but the default Courier for
monospaced text is somewhat wide.)
-- Brian D. Ripley,? ? ? ? ?
? ? ? ? ripley at 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
Brian D. Ripley, ripley at 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
True. A markup command won't be enough to do the job. A function is needed to count the character number (based on the font and size) and if it is greater than the width of the page (based on A4 format or US letter), it will split the line. Now another question regarding the code in the \examples field: how to keep the same format as the source code because all lines start vertically at the same position? for ex, if I have tab set manually in the source code, it is ignored in the pdf manual file. Do I have to use \tab? How about html help page? I have noticed that there is one file 00Index.html in html folder. I didn't have any error message when I ran R CMD check and build. But it seems that other html files missing. How to repair? when I ran R CMD check, the pdf manual file was created in one level up the package folder. I moved it to help folder. How to set options so that it will be created in the help folder? thanks,
--- On Wed, 9/22/10, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
From: Prof Brian Ripley <ripley at stats.ox.ac.uk> Subject: Re: [Rd] some problems reported in 00check.log To: "carol white" <wht_crl at yahoo.com> Cc: "Uwe Ligges" <ligges at statistik.tu-dortmund.de>, r-devel at r-project.org Date: Wednesday, September 22, 2010, 5:04 AM On Wed, 22 Sep 2010, carol white wrote:
So there is no sort of automatic way like using a
markup command for the susceptible fields instead of splitting manually a line on different lines? Well, how is the automatic command to know how to do this?? As you will see from the autmatic wrapping in e.g. deparse(), we are not able to do a very good job. There has been some talk about doing this automatically as a backstop, but I don't know the current state: in any case it does not happen in released versions of R.
True that this doesn't happen in Arguments field (I
confused with
Format field). Also true that the codes used in Usage, Examples etc
are in
courrier. Is there any way to reduce the size and not
to change the
font of character for these fields?
You can change Rd.sty, which already contains options for using other fontsets.
Best, Carol --- On Wed, 9/22/10, Prof Brian Ripley <ripley at stats.ox.ac.uk>
wrote:
From: Prof Brian Ripley <ripley at stats.ox.ac.uk> Subject: Re: [Rd] some problems reported in
00check.log
To: "carol white" <wht_crl at yahoo.com> Cc: "Uwe Ligges" <ligges at statistik.tu-dortmund.de>,
r-devel at r-project.org
Date: Wednesday, September 22, 2010, 2:15 AM On Wed, 22 Sep 2010, carol white wrote:
Thank you very much Uwe. It works now. I have a question about pdf formating in pdf
manual
file:
How to format the long lines which go to the
margin?
For ex, this happens in Usage field if a function
has many
arguments. Also, it happens in examples or
Arugment sections
when the lines are long. Correct the sources by re-formatting over-long
lines
yourself.? (This should only happen in
verbatim-like
sections, hence unlikely to happen in
\argument{}.)
One of the things we suggest when checking a
package is to
read through the PDF manual, and this is one of
the problems
to look out for.? (Note that it does depend on
the
fonts used for the PDF, but the default Courier
for
monospaced text is somewhat wide.) -- Brian D. Ripley,? ? ? ? ? ? ? ? ? ripley at 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
-- Brian D. Ripley,? ? ? ? ? ? ? ? ? ripley at 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
On 23.09.2010 09:20, carol white wrote:
True. A markup command won't be enough to do the job. A function is needed to count the character number (based on the font and size) and if it is greater than the width of the page (based on A4 format or US letter), it will split the line. Now another question regarding the code in the \examples field: how to keep the same format as the source code because all lines start vertically at the same position? for ex, if I have tab set manually in the source code, it is ignored in the pdf manual file. Do I have to use \tab? How about html help page?
>
I have noticed that there is one file 00Index.html in html folder. I didn't have any error message when I ran R CMD check and build. But it seems that other html files missing. How to repair?
If this is R > 2.10.0, it is expected. Static html files are not generated upon installation any more. Contents is generated dynamically upon request now.
when I ran R CMD check, the pdf manual file was created in one level up the package folder. I moved it to help folder. How to set options so that it will be created in the help folder?
The pdf manual is not part of a binary package. A user can ask R to generate the manual or parts of it. The manual will so be generated by CRAN, for example. Uwe Ligges
thanks, --- On Wed, 9/22/10, Prof Brian Ripley<ripley at stats.ox.ac.uk> wrote:
From: Prof Brian Ripley<ripley at stats.ox.ac.uk> Subject: Re: [Rd] some problems reported in 00check.log To: "carol white"<wht_crl at yahoo.com> Cc: "Uwe Ligges"<ligges at statistik.tu-dortmund.de>, r-devel at r-project.org Date: Wednesday, September 22, 2010, 5:04 AM On Wed, 22 Sep 2010, carol white wrote:
So there is no sort of automatic way like using a
markup command for the susceptible fields instead of splitting manually a line on different lines? Well, how is the automatic command to know how to do this? As you will see from the autmatic wrapping in e.g. deparse(), we are not able to do a very good job. There has been some talk about doing this automatically as a backstop, but I don't know the current state: in any case it does not happen in released versions of R.
True that this doesn't happen in Arguments field (I
confused with
Format field). Also true that the codes used in Usage, Examples etc
are in
courrier. Is there any way to reduce the size and not
to change the
font of character for these fields?
You can change Rd.sty, which already contains options for using other fontsets.
Best, Carol --- On Wed, 9/22/10, Prof Brian Ripley<ripley at stats.ox.ac.uk>
wrote:
From: Prof Brian Ripley<ripley at stats.ox.ac.uk> Subject: Re: [Rd] some problems reported in
00check.log
To: "carol white"<wht_crl at yahoo.com> Cc: "Uwe Ligges"<ligges at statistik.tu-dortmund.de>,
r-devel at r-project.org
Date: Wednesday, September 22, 2010, 2:15 AM On Wed, 22 Sep 2010, carol white wrote:
Thank you very much Uwe. It works now. I have a question about pdf formating in pdf
manual
file:
How to format the long lines which go to the
margin?
For ex, this happens in Usage field if a function
has many
arguments. Also, it happens in examples or
Arugment sections
when the lines are long. Correct the sources by re-formatting over-long
lines
yourself. (This should only happen in
verbatim-like
sections, hence unlikely to happen in
\argument{}.)
One of the things we suggest when checking a
package is to
read through the PDF manual, and this is one of
the problems
to look out for. (Note that it does depend on
the
fonts used for the PDF, but the default Courier
for
monospaced text is somewhat wide.)
-- Brian D. Ripley,
ripley at 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
--
Brian D. Ripley,
ripley at 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
I used the 2.10.0 version
--- On Thu, 9/23/10, Uwe Ligges <ligges at statistik.tu-dortmund.de> wrote:
From: Uwe Ligges <ligges at statistik.tu-dortmund.de> Subject: Re: [Rd] some problems reported in 00check.log To: "carol white" <wht_crl at yahoo.com> Cc: "Prof Brian Ripley" <ripley at stats.ox.ac.uk>, r-devel at r-project.org Date: Thursday, September 23, 2010, 4:57 AM
If this is R > 2.10.0, it is expected. Static html files are not generated upon installation any more. Contents is generated dynamically upon request now.
On 23.09.2010 18:16, carol white wrote:
I used the 2.10.0 version
My apologies, I actually meant R >= 2.10.0 and hence it is not a surprise. Best, Uwe Ligges
--- On Thu, 9/23/10, Uwe Ligges<ligges at statistik.tu-dortmund.de> wrote:
From: Uwe Ligges<ligges at statistik.tu-dortmund.de> Subject: Re: [Rd] some problems reported in 00check.log To: "carol white"<wht_crl at yahoo.com> Cc: "Prof Brian Ripley"<ripley at stats.ox.ac.uk>, r-devel at r-project.org Date: Thursday, September 23, 2010, 4:57 AM
If this is R> 2.10.0, it is expected. Static html files are not generated upon installation any more. Contents is generated dynamically upon request now.