"R" help leaves out lines of text

"R" help leaves out lines of text

[paul]

I am ramping up on the R statistical analysis environment.  I find that the 
help leaves out entire lines of text.  The pager is /usr/lib/R/bin/pager.  
I changed it to /bin/less, but I see the same symptom.  The problem shows 
up both in xterm and mintty.  The computer is in a locked down environment, 
so a straight update of cygwin packages is not an option.  From the R 
forum, the problem might be due to improper handling of line endings by the 
R port to cygwin.

Is there anything further I can try to circumvent the problem?

My version info is:

   64-bit Cygwin DLL version 1.7.28
   R version 3.0.1-1


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Re: "R" help leaves out lines of text

[Marco Atzeri]

On 4/16/2015 4:22 PM, paul wrote:
> I am ramping up on the R statistical analysis environment.  I find that the
> help leaves out entire lines of text.  The pager is /usr/lib/R/bin/pager.
> I changed it to /bin/less, but I see the same symptom.  The problem shows
> up both in xterm and mintty.  The computer is in a locked down environment,
> so a straight update of cygwin packages is not an option.  From the R
> forum, the problem might be due to improper handling of line endings by the
> R port to cygwin.
>
> Is there anything further I can try to circumvent the problem?
>
> My version info is:
>
>     64-bit Cygwin DLL version 1.7.28
>     R version 3.0.1-1
>

Are the input files Unix style or DOS style ?
Can you give an example to replicate your finding ?

I can that test than if the last R-3.1.3-1 package behaves correctly
or not. R-3.0.1-1 package is almost 2 years old.


Regards
Marco







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Re: "R" help leaves out lines of text

[paul]

Marco Atzeri <marco.atzeri <at> gmail.com> writes:
>> I am ramping up on the R statistical analysis environment.  I find
>> that the help leaves out entire lines of text.  The pager is
>> /usr/lib/R/bin/pager.  I changed it to /bin/less, but I see the
>> same symptom.  The problem shows up both in xterm and mintty.  The
>> computer is in a locked down environment, so a straight update of
>> cygwin packages is not an option.  From the R forum, the problem
>> might be due to improper handling of line endings by the R port to
>> cygwin.
>>
>> Is there anything further I can try to circumvent the problem?
>>
>> My version info is:
>>
>>     64-bit Cygwin DLL version 1.7.28
>>     R version 3.0.1-1
>>
> 
> Are the input files Unix style or DOS style ?
> Can you give an example to replicate your finding ?
> 
> I can that test than if the last R-3.1.3-1 package behaves correctly
> or not. R-3.0.1-1 package is almost 2 years old.

I can't actually find the help files; I suspect that they are not just
plain text.  I tried looking for html versions of the help pages by
ferruting through the R.home() subtree.  Haven't found them so far.
There are package pages in subdirectories <package>/html/00Index.html,
but they just contain links to html files that don't reside in my
R.home() subtree.  There are also subdirectories <package>/help, but
they contain pages that I don't recognize (*.rds, *.rdb, *.rdx).

As an example, I've attached the output from ?help at the very end
below.  My current workaround is to use the following in my
~/.Rprofile, which forces the help to a browser:

   options(browser="cygstart")
   options(help_type="html")

Here's the bad result from help(help,help_type="text"):


 help                   package:utils                   R Documentation

<....multiple blank lines...>

Documentation

<....multiple blank lines...>

Description:

<....multiple blank lines...>

Usage:

<....multiple blank lines...>

     help(topic, package = NULL, lib.loc = NULL,
          verbose = getOption("verbose"),
          try.all.packages = getOption("help.try.all.packages"),
          help_type = getOption("help_type"))

<....multiple blank lines...>

Arguments:

<....multiple blank lines...>

lines 1-23------------------------- ("less" prompt)

<....multiple blank lines...>

Details:

<....multiple blank lines...>

     The following types of help are available:

<....multiple blank lines...>

Plain text help

<....multiple blank lines...>

If a package is specified, (text or, in interactive use only, HTML)
          information on the package, including hints/links to suitable
          help topics.

<....multiple blank lines...>

lines 24-46------------------------- ("less" prompt)

<....multiple blank lines...>

Offline help:

<....multiple blank lines...>

Note:

<....multiple blank lines...>

References:

<....multiple blank lines...>

     Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) _The New S
     Language_.  Wadsworth & Brooks/Cole.

<....multiple blank lines...>

See Also:

<....multiple blank lines...>

Examples:

<....multiple blank lines...>

     help()
     help(help)              # the same

<....multiple blank lines...>

lines 47-69------------------------- ("less" prompt)
      help(lapply)

<....multiple blank lines...>

     help("for")             # or ?"for", but quotes/backticks are needed

<....multiple blank lines...>

     try({# requires working TeX installation:
      help(dgamma, help_type = "pdf")
      ## -> nicely formatted pdf -- including math formula -- for help
(dgamma):
      system2(getOption("pdfviewer"), "dgamma.pdf", wait = FALSE)
     })

<....multiple blank lines...>

     help(package = "splines") # get help even when package is not loaded

<....multiple blank lines...>

     topi <- "women"
     help(topi)

<....multiple blank lines...>

     try(help("bs", try.all.packages = FALSE)) # reports not found (an 
error)
     help("bs", try.all.packages = TRUE)       # reports can be found
                                               # in package 'splines'

<....multiple blank lines...>

     ## For programmatic use:
     topic <- "family"; pkg_ref <- "stats"
     help((topic), (pkg_ref))

<....multiple blank lines...>

lines 70-92------------------------- ("less" prompt)

<....multiple blank lines...>

     help("for")             # or ?"for", but quotes/backticks are needed

<....multiple blank lines...>

     try({# requires working TeX installation:
      help(dgamma, help_type = "pdf")
      ## -> nicely formatted pdf -- including math formula -- for help
(dgamma):
      system2(getOption("pdfviewer"), "dgamma.pdf", wait = FALSE)
     })

<....multiple blank lines...>

     help(package = "splines") # get help even when package is not loaded

<....multiple blank lines...>

     topi <- "women"
     help(topi)

<....multiple blank lines...>

     try(help("bs", try.all.packages = FALSE)) # reports not found (an 
error)
     help("bs", try.all.packages = TRUE)       # reports can be found
                                               # in package 'splines'

<....multiple blank lines...>

     ## For programmatic use:
     topic <- "family"; pkg_ref <- "stats"
     help((topic), (pkg_ref))

<....multiple blank lines...>

lines 71-93/93 (END)------------------------- ("less" prompt)


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Re: "R" help leaves out lines of text

[Marco Atzeri]

On 4/17/2015 8:57 PM, paul wrote:
> Marco Atzeri <marco.atzeri <at> gmail.com> writes:
>>> I am ramping up on the R statistical analysis environment.  I find
>>> that the help leaves out entire lines of text.  The pager is
>>> /usr/lib/R/bin/pager.  I changed it to /bin/less, but I see the
>>> same symptom.  The problem shows up both in xterm and mintty.  The
>>> computer is in a locked down environment, so a straight update of
>>> cygwin packages is not an option.  From the R forum, the problem
>>> might be due to improper handling of line endings by the R port to
>>> cygwin.
>>>
>>> Is there anything further I can try to circumvent the problem?
>>>
>>> My version info is:
>>>
>>>      64-bit Cygwin DLL version 1.7.28
>>>      R version 3.0.1-1
>>>
>>
>> Are the input files Unix style or DOS style ?
>> Can you give an example to replicate your finding ?
>>
>> I can that test than if the last R-3.1.3-1 package behaves correctly
>> or not. R-3.0.1-1 package is almost 2 years old.
>
> I can't actually find the help files;

the documentation is available as info files.

$ cygcheck -l R |grep info
/usr/share/info/R-admin.info.gz
/usr/share/info/R-data.info.gz
/usr/share/info/R-exts.info-1.gz
/usr/share/info/R-exts.info-2.gz
/usr/share/info/R-exts.info.gz
/usr/share/info/R-FAQ.info.gz
/usr/share/info/R-intro.info.gz
/usr/share/info/R-ints.info.gz
/usr/share/info/R-lang.info.gz

For what I can see the help data are also present.
The formatting could be better but I have no problem in reading.

If you are looking for a HTML browser help,
of course it is not configured.

Regards
Marco












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