[R] having trouble with "R CMD INSTALL"

From: Gene Leynes <gleynes+r_at_gmail.com>
Date: Mon, 18 Apr 2011 18:55:01 -0500


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>

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