Hi, I wonder what is a better way to organize a lot of R source files. I have a lot of utility functions written and store them in several source files (e.g util1.R, util2.R,..utilN.R). I also have a master file in which the source command is used to load all the util.R files. When I need to use the utility functions in a new project, I create a new R file (e.g main.R) in which I "source" the master file. The problem with this approach is that anytime a single utility function is modified, I need to rerun the source command in main.R to load the master file, which loads all the utility R files via a loop over each file. Sometimes I have to wait for 10 seconds to get them all loaded. Sometimes I forget to run the source command. Is there a way in R to 1) only reload the file changed (like a make utility) when I run source on all utility files and/or even better 2) reload the changed utility files, when I run a command that use one of those utility functions, without the need for me to source those files. Not sure if packaging solves this issue because the library command has be used every time a utility function is modified and in addition the package has to be rebuilt. I don't worry about sharing the source files at this moment as I am the only user of those utility files. This may be a common issue many R users face. I wonder how other R users solve this issue. thanks Jeff
Hi Jeff,
Your request makes a lot of sense. I often modify files in the packages
I maintain, typically by loading the package, then working on a copy of
the function, continually "sourcing" the new code until it works
correctly, and then checking and building the package. Apart from the
official packages I maintain, I keep a few local packages with odd
functions that I don't think are worth uploading to an already loaded
CRAN. This shell script can be used to automate the building of a package.
#!/bin/sh
cp $1 $2/R
if R CMD check $2; then
R CMD build $2;
R CMD INSTALL $3;
else
echo "Problem with R check of $2"
fi
If I had modified the "clinsig.R" file in the clinsig package, I could
call this script like this:
Rpackage /home/jim/R/clinsig.R /home/jim/R/clinsig clinsig_1.0-1.tar.gz
and it would rebuild the package with the new function. Because I
usually keep the files I am modifying in /home/jim/R I could simplify
the command line a bit. This may seem like a lot of work, but when I
worked out a way to get a function to check the timestamp of its source
file and compare it against the timestamp of the latest package:
if(max(file.info(system("find /home/jim/R -name 'clinsig.R'
-type f",intern=TRUE))$mtime) >
max(file.info(system("find /home/jim/R -name 'clinsig_*'
-type f",intern=TRUE))$mtime))
source("/home/jim/R/clinsig.R")
a lot of hard coding of file locations ends up in your function file.
Jim
library("R.utils");
sourceDirectory("myRFiles/", modifiedOnly=TRUE);
See ?sourceDirectory (regardless what the Rd help say, any '...'
argument is passed to sourceTo()).
/Henrik
On Fri, Jan 8, 2010 at 7:38 AM, Hao Cen <hcen at andrew.cmu.edu>
wrote:> Hi,
>
> I wonder what is a better way to organize a lot of R source files. I have
> a lot of utility functions written and store them in several source files
> (e.g util1.R, util2.R,..utilN.R). I also have a master file in which the
> source command is used to load all the util.R files. When I need to use
> the utility functions in a new project, I create a new R file (e.g main.R)
> in which I "source" the master file.
>
> The problem with this approach is that anytime a single utility function
> is modified, I need to rerun the source command in main.R to load the
> master file, which loads all the utility R files via a loop over each
> file. Sometimes I have to wait for 10 seconds to get them all loaded.
> Sometimes I forget to run the source command. Is there a way in R to 1)
> only reload the file changed (like a make utility) when I run source on
> all utility files and/or even better 2) ?reload the changed utility files,
> when I run a command that use one of those utility functions, without the
> need for me to source those files.
>
> Not sure if packaging solves this issue because the library command has be
> used every time a utility function is modified and in addition the package
> has to be rebuilt. I don't worry about sharing the source files at this
> moment as I am the only user of those utility files.
>
> This may be a common issue many R users face. I wonder how other R users
> solve this issue.
>
> thanks
>
> Jeff
>
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