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Markus Weisner

2010-Jan-06 01:15 UTC

[R] debugging package

I am trying to debug a package to submit it to CRAN and am getting a bunch
of error messages.  Most of the errors are because of the Rd files which
were automatically populated by the package.skeleton function.  I find the
section on documentation to be pretty confusion in the R Extensions manual.
Any help on getting these errors fixed would be hugely appreciated.  Thanks.
--Markus

* checking for working pdflatex ... OK
* using log directory '/Users/markus/Dropbox/NFIRS_S4/NFIRS.Rcheck'
* using R version 2.9.2 Patched (2009-09-24 r50179)
* using session charset: UTF-8
* checking for file 'NFIRS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NFIRS' version '1.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for executable files ... OK
* checking whether package 'NFIRS' can be installed ... WARNING
Found the following significant warnings:
       missing link(s):  ~~fun~~ CLASSNAME-class
See '/Users/markus/Dropbox/NFIRS_S4/NFIRS.Rcheck/00install.out' for
details.
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... ERROR
Rd files with likely Rd problems:
Unaccounted top-level text in file 'NFIRS-class.Rd':
Following section 'note':
"\n\n ~Make other sections like Warning with \\section{Warning }{....}
~\n\n"

Unaccounted top-level text in file 'NFIRS-package.Rd':
Following section 'references':
"\n~~ Optionally other standard keywords, one per line, from file KEYWORDS
in the R documentation directory ~~\n"

Rd files with missing or empty '\title':
  NFIRS.summary.Rd
  read.NFIRS.Rd

Rd files without 'description':
  NFIRS.summary.Rd
  read.NFIRS.Rd
Rd files without 'title':
  NFIRS.summary.Rd
  read.NFIRS.Rd
These entries are required in an Rd file.

Rd files with non-standard keywords:
  as.data.frame-methods.Rd: ~~ other possible keyword(s)
  head-methods.Rd: ~~ other possible keyword(s)
  NFIRS.summary.Rd: ~kwd1 ~kwd2
  read.NFIRS.Rd: ~kwd1 ~kwd2
  summary-methods.Rd: ~~ other possible keyword(s)
  tail-methods.Rd: ~~ other possible keyword(s)
Each '\keyword' entry should specify one of the standard keywords (as
listed in file 'KEYWORDS' in the R documentation directory).

Rd files with duplicated alias 'as.data.frame,NFIRS-method':
  as.data.frame-methods.Rd NFIRS-class.Rd
Rd files with duplicated alias 'head,NFIRS-method':
  head-methods.Rd NFIRS-class.Rd
Rd files with duplicated alias 'summary,NFIRS-method':
  NFIRS-class.Rd summary-methods.Rd
Rd files with duplicated alias 'tail,NFIRS-method':
  NFIRS-class.Rd tail-methods.Rd

See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.

	[[alternative HTML version deleted]]

Uwe Ligges

2010-Jan-06 10:03 UTC

head link

[R] debugging package

On 06.01.2010 02:15, Markus Weisner wrote:> I am trying to debug a package to submit it to CRAN and am getting a bunch
> of error messages.  Most of the errors are because of the Rd files which
> were automatically populated by the package.skeleton function.  I find the
> section on documentation to be pretty confusion in the R Extensions manual.
> Any help on getting these errors fixed would be hugely appreciated. 
Thanks.
> --Markus
>
> * checking for working pdflatex ... OK
> * using log directory '/Users/markus/Dropbox/NFIRS_S4/NFIRS.Rcheck'
> * using R version 2.9.2 Patched (2009-09-24 r50179)
> * using session charset: UTF-8
> * checking for file 'NFIRS/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'NFIRS' version '1.0'
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking for executable files ... OK
> * checking whether package 'NFIRS' can be installed ... WARNING
> Found the following significant warnings:
>         missing link(s):  ~~fun~~ CLASSNAME-class

You are supposed to fill in documentation and delete the examples such 
as "~~fun~~" while filling in appropriate things.

> See '/Users/markus/Dropbox/NFIRS_S4/NFIRS.Rcheck/00install.out' for
details.
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking top-level files ... OK
> * checking index information ... OK
> * checking package subdirectories ... OK
> * checking R files for non-ASCII characters ... OK
> * checking R files for syntax errors ... OK
> * checking whether the package can be loaded ... OK
> * checking whether the package can be loaded with stated dependencies ...
OK
> * checking for unstated dependencies in R code ... OK
> * checking S3 generic/method consistency ... OK
> * checking replacement functions ... OK
> * checking foreign function calls ... OK
> * checking R code for possible problems ... OK
> * checking Rd files ... ERROR
> Rd files with likely Rd problems:
> Unaccounted top-level text in file 'NFIRS-class.Rd':
> Following section 'note':
> "\n\n ~Make other sections like Warning with \\section{Warning }{....}
> ~\n\n"
Well this tells *you* how to make other sections. Just delete that part.

>
> Unaccounted top-level text in file 'NFIRS-package.Rd':
> Following section 'references':
> "\n~~ Optionally other standard keywords, one per line, from file
KEYWORDS
> in the R documentation directory ~~\n"

Same as above.
> Rd files with missing or empty '\title':
>    NFIRS.summary.Rd
>    read.NFIRS.Rd
 From here the messages are quite self explaining, I think.

Uwe Ligges


> Rd files without 'description':
>    NFIRS.summary.Rd
>    read.NFIRS.Rd
> Rd files without 'title':
>    NFIRS.summary.Rd
>    read.NFIRS.Rd
> These entries are required in an Rd file.
>
> Rd files with non-standard keywords:
>    as.data.frame-methods.Rd: ~~ other possible keyword(s)
>    head-methods.Rd: ~~ other possible keyword(s)
>    NFIRS.summary.Rd: ~kwd1 ~kwd2
>    read.NFIRS.Rd: ~kwd1 ~kwd2
>    summary-methods.Rd: ~~ other possible keyword(s)
>    tail-methods.Rd: ~~ other possible keyword(s)
> Each '\keyword' entry should specify one of the standard keywords
(as
> listed in file 'KEYWORDS' in the R documentation directory).
>
> Rd files with duplicated alias 'as.data.frame,NFIRS-method':
>    as.data.frame-methods.Rd NFIRS-class.Rd
> Rd files with duplicated alias 'head,NFIRS-method':
>    head-methods.Rd NFIRS-class.Rd
> Rd files with duplicated alias 'summary,NFIRS-method':
>    NFIRS-class.Rd summary-methods.Rd
> Rd files with duplicated alias 'tail,NFIRS-method':
>    NFIRS-class.Rd tail-methods.Rd
>
> See the chapter 'Writing R documentation files' in manual
'Writing R
> Extensions'.
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Liviu Andronic

2010-Jan-06 10:11 UTC

head link

[R] debugging package

Hello

On 1/6/10, Markus Weisner <public.markus at mac.com>
wrote:>  * checking whether package 'NFIRS' can be installed ... WARNING
>  Found the following significant warnings:
>        missing link(s):  ~~fun~~ CLASSNAME-class
>  See '/Users/markus/Dropbox/NFIRS_S4/NFIRS.Rcheck/00install.out'
for details.
>I am not sure what this is about.

>  * checking Rd files ... ERROR
>  Rd files with likely Rd problems:
>  Unaccounted top-level text in file 'NFIRS-class.Rd':
>  Following section 'note':
>  "\n\n ~Make other sections like Warning with \\section{Warning
}{....}
>  ~\n\n"
>I suspect that top-level text concerns all text not included in .Rd
tags. If you look at an .Rd file from another package [1], all the
text other than comments will be inside \some_command{}.

[1]
http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/RcmdrPlugin.sos/man/sosInit.Rd?rev=162&root=rsitesearch&view=markup

>  Unaccounted top-level text in file 'NFIRS-package.Rd':
>  Following section 'references':
>  "\n~~ Optionally other standard keywords, one per line, from file
KEYWORDS
>  in the R documentation directory ~~\n"
>
>  Rd files with missing or empty '\title':
>   NFIRS.summary.Rd
>   read.NFIRS.Rd
>It seems you need to add \title{} in each .Rd file (again, see a CRAN
package example).
>  Rd files without 'description':
>   NFIRS.summary.Rd
>   read.NFIRS.Rd
>You need to provide \description{} as well. You need to describe your
functions at a minimum.

>  Rd files without 'title':
>   NFIRS.summary.Rd
>   read.NFIRS.Rd
>  These entries are required in an Rd file.
>
>  Rd files with non-standard keywords:
>   as.data.frame-methods.Rd: ~~ other possible keyword(s)
>   head-methods.Rd: ~~ other possible keyword(s)
>   NFIRS.summary.Rd: ~kwd1 ~kwd2
>   read.NFIRS.Rd: ~kwd1 ~kwd2
>   summary-methods.Rd: ~~ other possible keyword(s)
>   tail-methods.Rd: ~~ other possible keyword(s)
>  Each '\keyword' entry should specify one of the standard keywords
(as
>  listed in file 'KEYWORDS' in the R documentation directory).
>You need to provide \keywords{}, taken strictly from the KEYWORDS file
(see the Manual).
Liviu
>  Rd files with duplicated alias 'as.data.frame,NFIRS-method':
>   as.data.frame-methods.Rd NFIRS-class.Rd
>  Rd files with duplicated alias 'head,NFIRS-method':
>   head-methods.Rd NFIRS-class.Rd
>  Rd files with duplicated alias 'summary,NFIRS-method':
>   NFIRS-class.Rd summary-methods.Rd
>  Rd files with duplicated alias 'tail,NFIRS-method':
>   NFIRS-class.Rd tail-methods.Rd
>
>  See the chapter 'Writing R documentation files' in manual
'Writing R
>  Extensions'.
>
>         [[alternative HTML version deleted]]
>
>  ______________________________________________
>  R-help at r-project.org mailing list
>  https://stat.ethz.ch/mailman/listinfo/r-help
>  PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>  and provide commented, minimal, self-contained, reproducible code.
>

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