stephen sefick
2010-Jul-14 21:03 UTC
[R] qplot in ggplot2 not working any longer - (what did I do?)
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()
--
Stephen Sefick
____________________________________
| Auburn University? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? |
| Department of Biological Sciences? ? ? ? ?? |
| 331 Funchess Hall? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? |
| Auburn, Alabama? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? |
| 36849? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? |
|___________________________________|
| sas0025 at auburn.edu? ? ? ? ? ? ? ? ? ? ? ? ? ?? |
| http://www.auburn.edu/~sas0025? ? ? ? ? ?? |
|___________________________________|
Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods.? We are mammals, and have not exhausted the
annoying little problems of being mammals.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -K. Mullis
Allan Engelhardt
2010-Jul-15 08:47 UTC
[R] qplot in ggplot2 not working any longer - (what did I do?)
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()
>
>
>
>
Hadley Wickham
2010-Jul-15 13:43 UTC
[R] qplot in ggplot2 not working any longer - (what did I do?)
For a quick fix, you probably need to reinstall plyr. Hadley On Wed, Jul 14, 2010 at 11:03 PM, stephen sefick <ssefick at gmail.com> 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() > > > > -- > Stephen Sefick > ____________________________________ > | Auburn University? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? | > | Department of Biological Sciences? ? ? ? ?? | > | 331 Funchess Hall? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > | Auburn, Alabama? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? | > | 36849? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > |___________________________________| > | sas0025 at auburn.edu? ? ? ? ? ? ? ? ? ? ? ? ? ?? | > | http://www.auburn.edu/~sas0025? ? ? ? ? ?? | > |___________________________________| > > Let's not spend our time and resources thinking about things that are > so little or so large that all they really do for us is puff us up and > make us feel like gods.? We are mammals, and have not exhausted the > annoying little problems of being mammals. > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -K. Mullis > > ______________________________________________ > R-help at 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. >-- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/