Re: [Rd] executable files R package

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Mon, 20 Feb 2012 17:39:04 +0000

On 20/02/2012 17:17, sahir bhatnagar wrote:
> thanks,
> I run into the following error message when running R CMD check
>
> "Source packages should not contain undeclared executable files"
>
> in reference to the following instruction from the help manual:
> "R CMD check will warn about them unless they are listed (one filepath per
> line) in a file BinaryFiles at the top level of the package."
>
> I created a file called 'BinaryFiles' placed in 'myPkg' directory.
> 'BinaryFiles' lists the path of the executable files that are included
> in myPkg/executables/win32. however I am still getting an error:
>
> Warning in readLines("BinaryFiles"): incomplete final line found on 'Binary
> Files'

That is a warning, not an error. And it means that you did not create the file correctly: ensure that you have an EOL mark (newline or CRLF depending on your OS) at the end of the last line.

> -Sahir
>
> On Fri, Feb 17, 2012 at 4:17 PM, William Dunlap<wdunlap_at_tibco.com> wrote:
>
>> If you put your prebuilt.exe into a directory under the
>> 'source' package's inst directory, say yourPkg/inst/executables/win32,
>> then the installed package will have them in in
>> yourPkg/executables/win32 and the user (via code you
>> write, presumably) can get the full path to the executable
>> in the installed package with
>> system.file(package="yourPkg", "executables", "win32", "prebuilt.exe").
>> Paste the output of that into the command given to system().
>>
>> Bill Dunlap
>> Spotfire, TIBCO Software
>> wdunlap tibco.com
>>
>>> -----Original Message-----
>>> From: r-devel-bounces_at_r-project.org [mailto:
>> r-devel-bounces_at_r-project.org] On Behalf Of sahir
>>> bhatnagar
>>> Sent: Friday, February 17, 2012 12:59 PM
>>> To: Duncan Murdoch
>>> Cc: r-devel_at_r-project.org
>>> Subject: Re: [Rd] executable files R package
>>>
>>> thanks,
>>> I will not submit to CRAN.
>>>
>>> I am having trouble going about including the .exe files in my package.
>>> > From the readings I see that the .exe files must be placed in a 'src'
>>> folder. But I don't see how I can access those files in R, without having
>>> to specify its path in the R command 'system'. I would like for the user
>> to
>>> only have to input a data file, which is then used in the .exe file.
>>>
>>> My problem is the following:
>>> Create a function which has two user inputs i.e. datasets: D1.txt and
>> D2.txt
>>> I have two '.exe' files i.e. E1.exe and E2.exe
>>>
>>> E1 takes in D1 and then outputs a text file say "text"
>>>
>>> then E2 takes in D2 and the "text", which outputs the result.
>>>
>>> Can this be done (even if it means having two functions) and then
>> assembled
>>> in a package, without the user having to specify the path of the .exe
>>> files, as well as the "text" that is outputted from running E1?
>>>
>>> Any direction as to how I can go about creating a package that would
>>> include these '.exe. files? I have only found documentation on calling .C
>>> code in R.
>>>
>>> Any help is much appreciated
>>>
>>> On Wed, Feb 15, 2012 at 10:14 AM, Duncan Murdoch
>>> <murdoch.duncan_at_gmail.com>wrote:
>>>
>>>> On 13/02/2012 2:36 PM, sahir bhatnagar wrote:
>>>>
>>>>> I am in the process of creating a package in R which calls
>>>>> pre-compiled C code i.e. '.exe' files in Windows.
>>>>>
>>>>> Since CRAN will not accept packages with binary code files, what are
>>>>> my options to meet the requirements while still including the
>>>>> executable file?
>>>>>
>>>>
>>>> I think you should ask the CRAN administrators that, but my
>> understanding
>>>> is that they are unlikely to accept your package as described. CRAN is
>>>> interested in platform-neutral packages, and if you have an .exe,
>> you're
>>>> going to be Windows-only.
>>>>
>>>> If you include the source code for that .exe and put together the
>> Makefile
>>>> to compile it, then they'd be more receptive, and someone might offer
>> help
>>>> to get it to run on other platforms if it doesn't on your first
>> attempt.
>>>>
>>>> If you don't want to include the .exe source (or can't), I think you
>>>> should just publish it on your own web page.
>>>>
>>>> Duncan Murdoch
>>>>
>>>> I read section 1.5.2 of the manual which mentions three options two of
>>>>> which involve negotiating with CRAN administrators. The third
>>>>> references the package Cairo which arranges to download additional
>>>>> software, but I don't see how this will allow my package to get
>>>>> accepted.
>>>>>
>>>>> It would seem that I need to ensure that my package works under both
>>>>> architectures (32 and 64 bit).
>>>>>
>>>>> 1) Would this be sufficient to get it accepted?
>>>>> 2) If so, does anyone have any documentation in performing this task,
>>>>> or can someone point me in the right direction?
>>>>>
>>>>> I was told that 'arulesSequences' is an example of a CRAN package
>>>>> while compiles executables. Was this package accepted because it
>>>>> worked under both architectures? or are there other reasons.
>>>>>
>>>>> thanks
>>>>>
>>>>> ______________________________**________________
>>>>> R-devel_at_r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/**listinfo/r-devel<
>> https://stat.ethz.ch/mailman/listinfo/r-devel>
>>>>>
>>>>
>>>>
>>>
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-- 
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

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