Stephen Sefick
2012-Nov-16 14:52 UTC
[R] source file on startup question - why does an old version of a function show up? ggplot or R?
All,
1. I will try and make this clear and concise. Please let me know any
information that would be helpful in figuring out this problem (I don't
know the relevant information to post). I am on linux- see below for
session information.
2. Problem:
working directory: home
an old version of a function is sourced into the R session and doesn't work
working directory: Desktop
the new version of the function is soured into the R session and works
3. I have setup a R_scripts folder that houses R scripts that I use on a
regular basis, and I have set up my .Rprofile (below) to source these
files when R is invoked.
What should I do?
.Rprofile:
###nothing yet###
print("It's go time")
#######################################################
#####source my R_scripts directory on start up#########
#######################################################
scripts2source <- dir("/home/user/R_scripts", full.names=TRUE)
R_scripts <- grep(".*\\.R$", scripts2source)
scripts2source <- scripts2source[R_scripts]
for(i in 1:length(scripts2source)){
source(scripts2source[i])
}
#######################################################
#######################################################
#######################################################
################set help_type##########################
#######################################################
options(help_type="html")
#######################################################
#######################################################
R session:
R version 2.15.2 (2012-10-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_0.9.2.1
loaded via a namespace (and not attached):
[1] colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 grid_2.15.2
[5] gtable_0.1.1 labeling_0.1 MASS_7.3-22 memoise_0.1
[9] munsell_0.3 plyr_1.7.1 proto_0.3-9.2
RColorBrewer_1.0-5
[13] reshape2_1.2.1 scales_0.2.2 stringr_0.6.1
--
Stephen Sefick
**************************************************
Auburn University
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
"A big computer, a complex algorithm and a long time does not equal
science."
-Robert Gentleman
R. Michael Weylandt
2012-Nov-16 15:14 UTC
[R] source file on startup question - why does an old version of a function show up? ggplot or R?
On Fri, Nov 16, 2012 at 2:52 PM, Stephen Sefick <sas0025 at auburn.edu> wrote:> All, > > 1. I will try and make this clear and concise. Please let me know any > information that would be helpful in figuring out this problem (I don't know > the relevant information to post). I am on linux- see below for session > information. > > 2. Problem: > working directory: home > > an old version of a function is sourced into the R session and doesn't work > > working directory: Desktop > > the new version of the function is soured into the R session and works > > 3. I have setup a R_scripts folder that houses R scripts that I use on a > regular basis, and I have set up my .Rprofile (below) to source these files > when R is invoked. > > What should I do? >Sounds like you've perhaps got a saved session in the home directory which is getting loaded after the profile and clobbering the newer version which isn't loaded when starting in other working directories. That or maybe there's redundancy in your startup scripts.... Wild guesses really, but it might be it. Cheers, MW
Stephen Sefick
2012-Nov-16 15:17 UTC
[R] source file on startup question - why does an old version of a function show up? ggplot or R?
Nothing like posting to the list to figure it out yourself. defined the little sourcing function in .Rprofile as the .First file. Now all is well. Sorry for clutering everyones email boxes. kind regards, Stephen Sefick On Fri 16 Nov 2012 08:52:00 AM CST, Stephen Sefick wrote:> > All, > > 1. I will try and make this clear and concise. Please let me know any > information that would be helpful in figuring out this problem (I > don't know the relevant information to post). I am on linux- see below > for session information. > > 2. Problem: > working directory: home > > an old version of a function is sourced into the R session and doesn't > work > > working directory: Desktop > > the new version of the function is soured into the R session and works > > 3. I have setup a R_scripts folder that houses R scripts that I use on > a regular basis, and I have set up my .Rprofile (below) to source > these files when R is invoked. > > What should I do? > > .Rprofile: > > ###nothing yet### > > print("It's go time") > > ####################################################### > #####source my R_scripts directory on start up######### > ####################################################### > > scripts2source <- dir("/home/user/R_scripts", full.names=TRUE) > R_scripts <- grep(".*\\.R$", scripts2source) > scripts2source <- scripts2source[R_scripts] > > for(i in 1:length(scripts2source)){ > source(scripts2source[i]) > } > > ####################################################### > ####################################################### > > > ####################################################### > ################set help_type########################## > ####################################################### > > options(help_type="html") > > ####################################################### > ####################################################### > > > > R session: > R version 2.15.2 (2012-10-26) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ggplot2_0.9.2.1 > > loaded via a namespace (and not attached): > [1] colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 grid_2.15.2 > [5] gtable_0.1.1 labeling_0.1 MASS_7.3-22 memoise_0.1 > [9] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 > [13] reshape2_1.2.1 scales_0.2.2 stringr_0.6.1 > > -- > Stephen Sefick > ************************************************** > Auburn University > 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 > > "A big computer, a complex algorithm and a long time does not equal science." > > -Robert Gentleman >