Re: [R] CGIwithR and visible output of 'invisible(capture.output(library(...)))'

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Sat 27 Jan 2007 - 21:48:40 GMT

I would not try uninstalling anything. The binary used is set via getOption("unzip"), and that in turn is set at R configure time and recorded in R_HOME/etc/Renviron. I have

R_UNZIPCMD=${R_UNZIPCMD-'/usr/bin/unzip'}

there. So you can alter that or set the environment variable in some other way.

The alternative is to alter R2HTML. R has zip.file.extract() which contains

         if (unzip != "internal") {
             if (!system(paste(unzip, "-o", file.path(path, zipname),
                 topic, "-d", tmpd, " > /dev/null")))
                 file <- file.path(tmpd, topic)
         }

and you will spot the crucial difference from R2HTML's myunzip().

Hope that helps!

On Sat, 27 Jan 2007, Leo Gürtler wrote:

> Prof Brian Ripley schrieb:
>
> Dear Prof Ripley,
>
> thanks for your information, in my first email I mentioned that I use
> Version 2.3.1 (2006-06-01) on ubuntu edgy. Sorry for leaving out the
> version-no. 1.1.2.3-13ubuntu2, together with R2HTML 1.58, installed
> directly from R via 'install.packages()'.
>
> Yes - you're right, there is a .deb called 'zlib-bin' which is
> responsible (binary called 'miniunzip'). The original 'unzip' you
> mention is also present but not used, because ->
>
> trying to deinstall 'zlib-bin' leads to unresolved dependencies with the
> _whole_ 'r-base-core' on ubuntu.

>
> This is totally unintelligible, because the man-page of miniunzip states
>
> "It was written as a demonstration of the zlib(3) library and
> therefore lack many of the features of the unzip(1) program."
>
> And - of course - there is no option like '-q' or '--q'.
>
> What are my opportunities besides the need to contact the
> ubuntu-maintainers to change the dependencies? There must be stated
> somewhere that R should call miniunzip instead of unzip to decompress
> files. Where can I find that option?

>
> Thanks!
>
> best,
>
> leo
>
>
>
>
>
>> This is done by .onLoad, so your settings are irrelevant.
>>
>> We have no information here on your platform, version of R, R2HTML or
>> anything else. But almost certainly the problem is the command given by
>> getOption("unzip"), which looks like an unzip clone not respecting the
>> -q flag.
>>
>> Try using the 'real' unzip () instead, from http://www.info-zip.org/.
>>
>>
>> On Sat, 27 Jan 2007, Leo Gürtler wrote:
>>
>>> Eric schrieb:
>>>> library(R2HTML, verbose = FALSE)
>>>>
>>>
>>> Dear Eric,
>>>
>>> thanks - I tried that, but that does not work for me. And it does not
>>> depend whether R2HTML is loaded via script/ batch job (-> webserver,
>>> cgi) or directly within R.
>>>
>>> The same happens (of course) by using
>>>
>>> require(R2HTML, quietly=TRUE)
>>>
>>> Are there any further options I missed?
>>> The problem seems to be that the file "R2HTMLstuff.zip" is extracted
>>> every time (although this is not necessary) - how can I ged rid of that?
>>>
>>> thanks,
>>>
>>> best,
>>>
>>> leo
>>>
>>>
>>> ----output----
>>>
>>>> library(R2HTML, verbose=FALSE)
>>> MiniUnz 1.01b, demo of zLib + Unz package written by Gilles Vollant
>>> more info at http://www.winimage.com/zLibDll/unzip.html
>>>
>>> /usr/local/lib/R/site-library/R2HTML/output/R2HTMLstuff.zip opened
>>> extracting: ASCIIMathML.js
>>> extracting: factor.gif
>>> extracting: gridR2HTML.css
>>> extracting: gridR2HTML.js
>>> extracting: numeric.gif
>>> extracting: Pastel.css
>>> extracting: R2HTML.css
>>> extracting: R2HTMLlogo.gif
>>> creating directory: runtime/
>>> creating directory: runtime/lib/
>>> extracting: runtime/lib/grid.js
>>> extracting: runtime/readme.txt
>>> creating directory: runtime/styles/
>>> creating directory: runtime/styles/classic/
>>> extracting: runtime/styles/classic/gecko.xml
>>> extracting: runtime/styles/classic/grid.css
>>> extracting: runtime/styles/classic/grid.png
>>> extracting: runtime/styles/classic/icons.png
>>> extracting: runtime/styles/classic/loading.gif
>>> creating directory: runtime/styles/flat/
>>> extracting: runtime/styles/flat/gecko.xml
>>> extracting: runtime/styles/flat/grid.css
>>> extracting: runtime/styles/flat/grid.png
>>> extracting: runtime/styles/flat/icons.png
>>> extracting: runtime/styles/flat/loading.gif
>>> creating directory: runtime/styles/xp/
>>> extracting: runtime/styles/xp/gecko.xml
>>> extracting: runtime/styles/xp/grid.css
>>> extracting: runtime/styles/xp/grid.png
>>> extracting: runtime/styles/xp/icons.png
>>> extracting: runtime/styles/xp/loading.gif
>>> extracting: SciViews.css
>>> extracting: tablesort.htc
>>>>
>>>
>>> ______________________________________________
>>> R-help@stat.math.ethz.ch 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.
>>>
>>
>

-- 
Brian D. Ripley,                  ripley@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


______________________________________________ R-help@stat.math.ethz.ch 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.

Received on Sun Jan 28 08:55:15 2007

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