The problem is that install.packages() and friends forks R and there is
no way to specify general options to that process (you can do the
configure.{args,vars} but nothing else).
One work-around could be to download the package and install it with R
--vanilla CMD INSTALL from the command line.
But it is probably better to fix your .Rprofile so it doesn't break the
install; see interactive() and commandArgs() for functions that may be
useful.
Hope this helps a little.
Allan
On 14/07/10 22:03, stephen sefick wrote:
This is the first time that I have tried to update packages with a
tinkered around with .Rprofile. I start R with R --vanilla and it
does not load my .Rprofile, but when I issue the command
update.packages() R downloads the packages as expected, but then seems
to load .Rprofile before compiling the packages sources. What am I
doing wrong?
kindest regards,
Stephen Sefick
see- Session info output and .Rprofile
Ubuntu 10.04
R 2.11.1
Session info:
R version 2.11.1 (2010-05-31)
x86_64-pc-linux-gnu
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] graphics grDevices utils datasets stats grid methods
[8] base
other attached packages:
[1] gpclib_1.5-1 StreamMetabolism_0.03-3 maptools_0.7-34
[4] lattice_0.18-8 sp_0.9-64 foreign_0.8-40
[7] chron_2.3-35 zoo_1.6-3 vegan_1.17-3
[10] ggplot2_0.8.8 proto_0.3-8 reshape_0.8.3
[13] plyr_0.1.9
.Rprofile:
#source USGS graphing function for base data
source("~/R_scripts/USGS.R")
source("~/R_scripts/publication_ggplot2_theme.R")
source("~/R_scripts/llScript.R")
#set help_type
options(help_type="html")
#exit to get around anoying q behavior
exit<- function(save="no"){q(save=save)}
#most used libraries
library(ggplot2)
library(vegan)
library(StreamMetabolism)
#allow gpclib package to be used
gpclibPermit()
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