Uwe,

It think the problem turned out to be with my "profile.site" file.

As I recall, temporarily deleting / renaming it was the simple fix.  I think
it had to do with something I use to parse the commandArgs

Thank you for your reply, and sorry for not responding sooner.  I didn't
think anyone responded!

Gene



2011/4/20 Uwe Ligges <ligges@statistik.tu-dortmund.de>

> Not sure what you are really doing, but
>
> R --vanilla CMD INSTALL something
>
> runs in a vanilla style. I just tested with a local .Rprofile under with
> R-2.13.0 under Windows.
> Perhaps it is specific to the package your are talking about? Perhaps you
> can make it available for further inspection of this problem?
>
> Uwe Ligges
>
>
>
>
>
> On 19.04.2011 01:55, Gene Leynes wrote:
>
>> Hello,
>>
>> I was having trouble passing in command line options when doing an package
>> install earlier.
>>
>>  From An Introduction in R
>>>
>>
>>  In addition, you can use25<
>>> http://cran.r-project.org/doc/manuals/R-intro.html#fn-25>options
>>>
>>> --arch=, --no-environ, --no-init-file, --no-site-file and
>>> --vanillabetween
>>> R and CMD: these affect any R processes run by the tools. (Here
>>> --vanillais equivalent to --no-environ
>>>
>>> --no-site-file --no-init-file.)
>>>
>>>  R CMD cmd arg
>>
>>
>> When I tried doing this, two unexpected things happened:
>>
>>    1. --vanilla doesn't have an effect when used with R CMD  (R --vanilla
>>
>>    CMD INSTALL rj_0.5.2-1.tar.gz)
>>    2. When loading my functions from "Rprofile.site" that seems to
>> interfere
>>
>>    with the INSTALL command.  I temporarily deleted the Rprofile.site
>> contents,
>>    and the install worked as expected.  Maybe it's because I'm also
>> parsing the
>>    arguments after the --args flag?
>>
>> The second item is probably "user error" on my part.
>> The first item seems like a possible R bug, but I'm not ruling out "user
>> error".  See "?user.error" for a sample error message
>>
>>
>> I finally got the package installed, but wanted to report this if it
>> really
>> is a bug.
>>
>>
>>
>> The lines below come from a DOS prompt:
>>
>> c:\Users\gene.leynes\Downloads>dir /B
>> gdata_2.8.1.zip
>> rj_0.5.2-1.tar.gz
>> c:\Users\gene.leynes\Downloads>R --vanilla
>>
>> R version 2.13.0 (2011-04-13)
>> Copyright (C) 2011 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>>   Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>  R.Version()
>>>
>> $platform
>> [1] "i386-pc-mingw32"
>>
>> $arch
>> [1] "i386"
>>
>> $os
>> [1] "mingw32"
>>
>> $system
>> [1] "i386, mingw32"
>>
>> $status
>> [1] ""
>>
>> $major
>> [1] "2"
>>
>> $minor
>> [1] "13.0"
>>
>> $year
>> [1] "2011"
>>
>> $month
>> [1] "04"
>>
>> $day
>> [1] "13"
>>
>> $`svn rev`
>> [1] "55427"
>>
>> $language
>> [1] "R"
>>
>> $version.string
>> [1] "R version 2.13.0 (2011-04-13)"
>>
>>  q()
>>>
>>
>> c:\Users\gene.leynes\Downloads>R --vanilla CMD INSTALL rj_0.5.2-1.tar.gz
>> Function_II.R :
>> Function_IM.R :
>> Function_NAsummary.R :
>> Function_YahooAdjCloseAsZoo.R :
>> Function_addbg.R :
>> Function_bgfun.R :
>> Function_boxplot2.R :
>> Function_clipdir.R :
>> Function_clipper.R :
>> Function_clipstar.R :
>> Function_comma.R :
>> Function_count.na.R :
>> Function_dftab.R :
>> Function_enclose.R :
>> Function_eye.R :
>> Function_factors.R :
>> Function_finder.R :
>> Function_headstr.R :
>> Function_inin.R :
>> Function_lll.R :
>> Function_loader.R :
>> Function_ma.R :
>> Function_makebm.R :
>> Function_makegm.R :
>> Function_makegroups.R :
>> Function_plot100colors.R :
>> Function_plotRunningSd.R :
>> Function_saver.R :
>> Function_sourcedir.R :
>> Function_stacker.R :
>> Function_subzoo.R :
>> Function_svr.R :
>> Function_tictoc.R :
>> Function_writexls.R :
>> Function_wtt_3.0.R :
>> heatplot.R :
>> loadfuns.R :
>> Opening: nextArgrj_0.5.2-1.tar.gz
>> Warning in file(file, "r", encoding = encoding) :
>>   cannot open file 'nextArgrj_0.5.2-1.tar.gz': No such file or directory
>> Error in file(file, "r", encoding = encoding) :
>>   cannot open the connection
>> Calls: source ->  file
>> Execution halted
>>
>> c:\Users\gene.leynes\Downloads>
>>
>>        [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help@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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