date:20190823

Re: [R-pkg-devel] Literal LaTeX Text in Function Arguments

2019-08-23 Thread bill

Hi Georgi,

Thanks for this pointer.  My guess at this point is that I've found a bug
(or maybe a couple of bugs with 'utils::prompt()' and with the Rd to help
conversion), but let me know if you think otherwise.

I just did that way, and the usage lines that were generated by
'utils::prompt()' and copied into the docs are:

topic_long_table_header(x, col_names = NULL,
  above_col_names = "\\hline", below_col_names = "\\hline",
  subsequent_page_notification = "\\ldots continued",
  latex_header = NULL, verbatim = NULL)

topic_long_table_footer(x, bottom_border = "\\hline",
  bottom_all_pages = NULL, bottom_last_page = NULL,
  subsequent_page_notification = "continued \\ldots",
  verbatim = NULL)

It is giving a very similar error with 'R CMD check' (outside devtools).
The escape of the backslashes appears to be needed, but "\\ldots" continues
to be translated into "...":

Codoc mismatches from documentation object 'topic_long_table_header':
topic_long_table_header
  Code: function(x, col_names = NULL, above_col_names = "\\hline",
 below_col_names = "\\hline",
 subsequent_page_notification = "\\ldots continued",
 latex_header = NULL, verbatim = NULL)
  Docs: function(x, col_names = NULL, above_col_names = "\hline",
 below_col_names = "\hline",
 subsequent_page_notification = "... continued",
 latex_header = NULL, verbatim = NULL)
  Mismatches in argument default values:
Name: 'above_col_names' Code: "\\hline" Docs: "\hline"
Name: 'below_col_names' Code: "\\hline" Docs: "\hline"
Name: 'subsequent_page_notification' Code: "\\ldots continued" Docs:
"... continued"
topic_long_table_footer
  Code: function(x, bottom_border = "\\hline", bottom_all_pages = NULL,
 bottom_last_page = NULL, subsequent_page_notification
 = "continued \\ldots", verbatim = NULL)
  Docs: function(x, bottom_border = "\hline", bottom_all_pages = NULL,
 bottom_last_page = NULL, subsequent_page_notification
 = "continued ...", verbatim = NULL)
  Mismatches in argument default values:
Name: 'bottom_border' Code: "\\hline" Docs: "\hline"
Name: 'subsequent_page_notification' Code: "continued \\ldots" Docs:
"continued ..."

Thanks,

Bill

-Original Message-
From: Georgi Boshnakov  
Sent: Friday, August 23, 2019 11:27 AM
To: b...@denney.ws; r-package-devel@r-project.org
Subject: RE: [R-pkg-devel] Literal LaTeX Text in Function Arguments

Hi Bill,

Sorry, I misunderstood the question.

To check if the problem is with R's tools, run
'utils::prompt(topic_long_table_header)" and see the usage section of the
generated file. Presumably, this should be the 'canonical way' to write the
usage entry for the function.
You can copy and paste it in the Rd file generated by roxygen2, then run 'R
CMD build' and 'R CMD check' (outside devtools). 

Georgi


-Original Message-
From: b...@denney.ws [mailto:b...@denney.ws]
Sent: 23 August 2019 15:27
To: Georgi Boshnakov; r-package-devel@r-project.org
Subject: RE: [R-pkg-devel] Literal LaTeX Text in Function Arguments

Hi Georgi,

I'm not trying to use it as part of my documentation, it is one of my
function arguments.  I want the function argument to be displayed correctly
in the help, but it is not.  I'm curious how I should document the
"subsequent_page_notification" function argument in Rd.

Specifically, the actual function definition (R code) looks like:

R code:
--
topic_long_table_header <- function(x,
col_names=NULL,
above_col_names="\\hline",
below_col_names="\\hline",
subsequent_page_notification="\\ldots
continued",
latex_header=NULL) {
  # The function body
}
--

So, I'm not trying to use LaTeX in the .Rd file; I'm trying to use it in R,
and I'm then copying it into the .Rd with extra escaping for the backslashes
(well, roxygen2 is doing the extra escaping).

Rd text
--
topic_long_table_header(x, col_names = NULL,
  above_col_names = "hline", below_col_names = "hline",
  subsequent_page_notification = "ldots continued",
  latex_header = NULL)
--

Thanks,

Bill

-Original Message-
From: Georgi Boshnakov 
Sent: Friday, August 23, 2019 9:52 AM
To: b...@denney.ws; r-package-devel@r-project.org
Subject: RE: [R-pkg-devel] Literal LaTeX Text in Function Arguments

Rd is not LaTeX, although it resembles it.  You should use only markup
described in WRE.
For example, \dots is for the use case you mention. 

Georgi Boshnakov





-Original Message-
From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On
Behalf Of b...@denney.ws
Sent: 23 August 2019 04:15
To: r-package-devel@r-project.org
Subject: [R-pkg-devel] Literal LaTeX Text in Function Arguments

Hello,

 

Does anyone know how to

Re: [R-pkg-devel] Literal LaTeX Text in Function Arguments

2019-08-23 Thread Georgi Boshnakov

Hi Bill,

Sorry, I misunderstood the question.

To check if the problem is with R's tools, run 
'utils::prompt(topic_long_table_header)" and see the usage section of the 
generated file. Presumably, this should be the 'canonical way' to write the 
usage entry for the function.
You can copy and paste it in the Rd file generated by roxygen2, then run 'R CMD 
build' and 'R CMD check' (outside devtools). 

Georgi


-Original Message-
From: b...@denney.ws [mailto:b...@denney.ws] 
Sent: 23 August 2019 15:27
To: Georgi Boshnakov; r-package-devel@r-project.org
Subject: RE: [R-pkg-devel] Literal LaTeX Text in Function Arguments

Hi Georgi,

I'm not trying to use it as part of my documentation, it is one of my
function arguments.  I want the function argument to be displayed correctly
in the help, but it is not.  I'm curious how I should document the
"subsequent_page_notification" function argument in Rd.

Specifically, the actual function definition (R code) looks like:

R code:
--
topic_long_table_header <- function(x,
col_names=NULL,
above_col_names="\\hline",
below_col_names="\\hline",
subsequent_page_notification="\\ldots
continued",
latex_header=NULL) {
  # The function body
}
--

So, I'm not trying to use LaTeX in the .Rd file; I'm trying to use it in R,
and I'm then copying it into the .Rd with extra escaping for the backslashes
(well, roxygen2 is doing the extra escaping).

Rd text
--
topic_long_table_header(x, col_names = NULL,
  above_col_names = "hline", below_col_names = "hline",
  subsequent_page_notification = "ldots continued",
  latex_header = NULL)
--

Thanks,

Bill

-Original Message-
From: Georgi Boshnakov  
Sent: Friday, August 23, 2019 9:52 AM
To: b...@denney.ws; r-package-devel@r-project.org
Subject: RE: [R-pkg-devel] Literal LaTeX Text in Function Arguments

Rd is not LaTeX, although it resembles it.  You should use only markup
described in WRE.
For example, \dots is for the use case you mention. 

Georgi Boshnakov





-Original Message-
From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On
Behalf Of b...@denney.ws
Sent: 23 August 2019 04:15
To: r-package-devel@r-project.org
Subject: [R-pkg-devel] Literal LaTeX Text in Function Arguments

Hello,

 

Does anyone know how to include verbatim \ldots (and maybe other LaTeX) in
an .Rd file correctly? 

 

When LaTeX is in the default arguments for a function, the code is
interpreted which makes the documentation not match the default formal
arguments.

 

An example is:

https://github.com/billdenney/TopicLongTableR/blob/1338116767d90e8211533cb6e
7db5ef30368dc33/R/topic_long_table_header_footer.R#L20

 

Which yields:

https://github.com/billdenney/TopicLongTableR/blob/1338116767d90e8211533cb6e
7db5ef30368dc33/man/topic_long_table_header.Rd#L10

 

Which gives the following warning with `devtools::check()`:

```

checking for code/documentation mismatches ... WARNING

Codoc mismatches from documentation object 'topic_long_table_header':

topic_long_table_header

  Code: function(x, col_names = NULL, above_col_names = "\\hline
 ",

 below_col_names = "\\hline  ",

 subsequent_page_notification = "\\ldots continued
 ",

 latex_header = NULL)

  Docs: function(x, col_names = NULL, above_col_names = "\\hline
 ",

 below_col_names = "\\hline  ",

 subsequent_page_notification = "\... continued",

 latex_header = NULL)

```

 

I'm not sure, but I think that the solution is to add more protection to the
\s when generating the roxygen or perhaps wrapping the arguments in some
form of verbatim block (if it's available).

 

Thanks,

 

Bill

 

P.S. This is also discussed in https://github.com/r-lib/roxygen2/issues/837
where it appears to be related to the conversion of .Rd to help files not
the roxygen step.

 


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Re: [R-pkg-devel] Literal LaTeX Text in Function Arguments

2019-08-23 Thread bill

Hi Georgi,

I'm not trying to use it as part of my documentation, it is one of my
function arguments.  I want the function argument to be displayed correctly
in the help, but it is not.  I'm curious how I should document the
"subsequent_page_notification" function argument in Rd.

Specifically, the actual function definition (R code) looks like:

R code:
--
topic_long_table_header <- function(x,
col_names=NULL,
above_col_names="\\hline",
below_col_names="\\hline",
subsequent_page_notification="\\ldots
continued",
latex_header=NULL) {
  # The function body
}
--

So, I'm not trying to use LaTeX in the .Rd file; I'm trying to use it in R,
and I'm then copying it into the .Rd with extra escaping for the backslashes
(well, roxygen2 is doing the extra escaping).

Rd text
--
topic_long_table_header(x, col_names = NULL,
  above_col_names = "hline", below_col_names = "hline",
  subsequent_page_notification = "ldots continued",
  latex_header = NULL)
--

Thanks,

Bill

-Original Message-
From: Georgi Boshnakov  
Sent: Friday, August 23, 2019 9:52 AM
To: b...@denney.ws; r-package-devel@r-project.org
Subject: RE: [R-pkg-devel] Literal LaTeX Text in Function Arguments

Rd is not LaTeX, although it resembles it.  You should use only markup
described in WRE.
For example, \dots is for the use case you mention. 

Georgi Boshnakov





-Original Message-
From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On
Behalf Of b...@denney.ws
Sent: 23 August 2019 04:15
To: r-package-devel@r-project.org
Subject: [R-pkg-devel] Literal LaTeX Text in Function Arguments

Hello,

 

Does anyone know how to include verbatim \ldots (and maybe other LaTeX) in
an .Rd file correctly? 

 

When LaTeX is in the default arguments for a function, the code is
interpreted which makes the documentation not match the default formal
arguments.

 

An example is:

https://github.com/billdenney/TopicLongTableR/blob/1338116767d90e8211533cb6e
7db5ef30368dc33/R/topic_long_table_header_footer.R#L20

 

Which yields:

https://github.com/billdenney/TopicLongTableR/blob/1338116767d90e8211533cb6e
7db5ef30368dc33/man/topic_long_table_header.Rd#L10

 

Which gives the following warning with `devtools::check()`:

```

checking for code/documentation mismatches ... WARNING

Codoc mismatches from documentation object 'topic_long_table_header':

topic_long_table_header

  Code: function(x, col_names = NULL, above_col_names = "\\hline
 ",

 below_col_names = "\\hline  ",

 subsequent_page_notification = "\\ldots continued
 ",

 latex_header = NULL)

  Docs: function(x, col_names = NULL, above_col_names = "\\hline
 ",

 below_col_names = "\\hline  ",

 subsequent_page_notification = "\... continued",

 latex_header = NULL)

```

 

I'm not sure, but I think that the solution is to add more protection to the
\s when generating the roxygen or perhaps wrapping the arguments in some
form of verbatim block (if it's available).

 

Thanks,

 

Bill

 

P.S. This is also discussed in https://github.com/r-lib/roxygen2/issues/837
where it appears to be related to the conversion of .Rd to help files not
the roxygen step.

 


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Re: [R-pkg-devel] Literal LaTeX Text in Function Arguments

2019-08-23 Thread Georgi Boshnakov

Rd is not LaTeX, although it resembles it.  You should use only markup 
described in WRE.
For example, \dots is for the use case you mention. 

Georgi Boshnakov





-Original Message-
From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf 
Of b...@denney.ws
Sent: 23 August 2019 04:15
To: r-package-devel@r-project.org
Subject: [R-pkg-devel] Literal LaTeX Text in Function Arguments

Hello,

 

Does anyone know how to include verbatim \ldots (and maybe other LaTeX) in
an .Rd file correctly? 

 

When LaTeX is in the default arguments for a function, the code is
interpreted which makes the documentation not match the default formal
arguments.

 

An example is:

https://github.com/billdenney/TopicLongTableR/blob/1338116767d90e8211533cb6e
7db5ef30368dc33/R/topic_long_table_header_footer.R#L20

 

Which yields:

https://github.com/billdenney/TopicLongTableR/blob/1338116767d90e8211533cb6e
7db5ef30368dc33/man/topic_long_table_header.Rd#L10

 

Which gives the following warning with `devtools::check()`:

```

checking for code/documentation mismatches ... WARNING

Codoc mismatches from documentation object 'topic_long_table_header':

topic_long_table_header

  Code: function(x, col_names = NULL, above_col_names = "\\hline
 ",

 below_col_names = "\\hline  ",

 subsequent_page_notification = "\\ldots continued
 ",

 latex_header = NULL)

  Docs: function(x, col_names = NULL, above_col_names = "\\hline
 ",

 below_col_names = "\\hline  ",

 subsequent_page_notification = "\... continued",

 latex_header = NULL)

```

 

I'm not sure, but I think that the solution is to add more protection to the
\s when generating the roxygen or perhaps wrapping the arguments in some
form of verbatim block (if it's available).

 

Thanks,

 

Bill

 

P.S. This is also discussed in https://github.com/r-lib/roxygen2/issues/837
where it appears to be related to the conversion of .Rd to help files not
the roxygen step.

 


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[R-pkg-devel] No protocol specified

2019-08-23 Thread Dr. rer. nat. Michael Thrun

Dear All,
I updated my package DataVisualizations and get a note, only for 
"r-release-osx-x86_64” and “r-oldrel-osx-x86_64”

Checking dependencies in R code ... NOTE
No protocol specified

Can anyone translate this note to me in a way that I know what the issue is?

Best Regards
Michael


Michael Thrun
Postdoctoral Scholar
Databionics AG,
Mathematics and Computer Science

Philipps-Universität Marburg
Hans-Meerwein-Straße 6, 04A28
D-35032 Marburg

Phone +49 6421/ 28 23922
www.uni-marburg.de/fb12/datenbionik/

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[R-pkg-devel] Literal LaTeX Text in Function Arguments

2019-08-23 Thread bill

Hello,

 

Does anyone know how to include verbatim \ldots (and maybe other LaTeX) in
an .Rd file correctly? 

 

When LaTeX is in the default arguments for a function, the code is
interpreted which makes the documentation not match the default formal
arguments.

 

An example is:

https://github.com/billdenney/TopicLongTableR/blob/1338116767d90e8211533cb6e
7db5ef30368dc33/R/topic_long_table_header_footer.R#L20

 

Which yields:

https://github.com/billdenney/TopicLongTableR/blob/1338116767d90e8211533cb6e
7db5ef30368dc33/man/topic_long_table_header.Rd#L10

 

Which gives the following warning with `devtools::check()`:

```

checking for code/documentation mismatches ... WARNING

Codoc mismatches from documentation object 'topic_long_table_header':

topic_long_table_header

  Code: function(x, col_names = NULL, above_col_names = "\\hline
 ",

 below_col_names = "\\hline  ",

 subsequent_page_notification = "\\ldots continued
 ",

 latex_header = NULL)

  Docs: function(x, col_names = NULL, above_col_names = "\\hline
 ",

 below_col_names = "\\hline  ",

 subsequent_page_notification = "\... continued",

 latex_header = NULL)

```

 

I'm not sure, but I think that the solution is to add more protection to the
\s when generating the roxygen or perhaps wrapping the arguments in some
form of verbatim block (if it's available).

 

Thanks,

 

Bill

 

P.S. This is also discussed in https://github.com/r-lib/roxygen2/issues/837
where it appears to be related to the conversion of .Rd to help files not
the roxygen step.

 


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Re: [R-pkg-devel] Literal LaTeX Text in Function Arguments

Re: [R-pkg-devel] Literal LaTeX Text in Function Arguments

Re: [R-pkg-devel] Literal LaTeX Text in Function Arguments

Re: [R-pkg-devel] Literal LaTeX Text in Function Arguments

[R-pkg-devel] No protocol specified

[R-pkg-devel] Literal LaTeX Text in Function Arguments

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