Re: [R] What is the most efficient practice to develop an R package?
On 10/26/2009 10:29 AM, Peng Yu wrote:
I am reading Section 5 and 6 of
http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf
It seems that I have to do the following two steps in order to make an
R package. But when I am testing these package, these two steps will
run many times, which may take a lot of time. So when I still develop
the package, shall I always source('linmod.R') to test it. Once the
code in linmod.R is finalized, then I run the following two steps?
I'm wondering what people usually do when developing packages.
1. Run the following command in R to create the package
package.skeleton(name=linmod, code_files=linmod.R)
2. Run the following command in shell to install
R CMD INSTALL -l /path/to/library linmod
You only do step 1 once, and you missed step 1.5: edit the files, which
comes before step 2.
I usually cycle between steps 1.5 and 2 multiple times. Sometimes I
will not repeat step 2, I'll put together a small script that includes
source('linmod.R')
environment(somefunction) - environment(linmod::somefunction)
and source that instead. The second line makes somefunction look for
functions in the namespace of the package; it's only useful if my edits
only affect one function, and the functions in the package never call
it: so usually I do the full install.
Duncan Murdoch
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Re: [R] What is the most efficient practice to develop an R package?
Peng Yu wrote:
I am reading Section 5 and 6 of
http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf
It seems that I have to do the following two steps in order to make an
R package. But when I am testing these package, these two steps will
run many times, which may take a lot of time. So when I still develop
the package, shall I always source('linmod.R') to test it. Once the
code in linmod.R is finalized, then I run the following two steps?
I'm wondering what people usually do when developing packages.
1. Run the following command in R to create the package
package.skeleton(name=linmod, code_files=linmod.R)
Do this once, to get a skeleton. Then edit the R source etc in the
created package.
2. Run the following command in shell to install
R CMD INSTALL -l /path/to/library linmod
see R CMD INSTALL --help and use options that minimize the amount of
non-essential work, e.g., no vignettes or documentation until that is
the focus of your development, or --libs-only if you are working on C
code. Use --clean to avoid stale package components. Develop individual
functions interactively, but write a script
library(MyPackage)
someFunction()
so that R -f myscript.R allows you to easily load your package and test
specific functionality in a clean R session.
Martin
__
R-help@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.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
__
R-help@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.
Re: [R] What is the most efficient practice to develop an R package?
On 26 October 2009 at 07:57, Martin Morgan wrote:
| Peng Yu wrote:
| I am reading Section 5 and 6 of
| http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf
|
| It seems that I have to do the following two steps in order to make an
| R package. But when I am testing these package, these two steps will
| run many times, which may take a lot of time. So when I still develop
| the package, shall I always source('linmod.R') to test it. Once the
| code in linmod.R is finalized, then I run the following two steps?
|
| I'm wondering what people usually do when developing packages.
|
|
| 1. Run the following command in R to create the package
| package.skeleton(name=linmod, code_files=linmod.R)
|
| Do this once, to get a skeleton. Then edit the R source etc in the
| created package.
|
| 2. Run the following command in shell to install
| R CMD INSTALL -l /path/to/library linmod
|
| see R CMD INSTALL --help and use options that minimize the amount of
| non-essential work, e.g., no vignettes or documentation until that is
| the focus of your development, or --libs-only if you are working on C
| code. Use --clean to avoid stale package components. Develop individual
| functions interactively, but write a script
|
| library(MyPackage)
| someFunction()
|
| so that R -f myscript.R allows you to easily load your package and test
| specific functionality in a clean R session.
With littler you can do without the one-off script as
$ r -lMyPackage -e'print(someFunction())'
runs both commands you would have put into script. Hence, I often do
something like
$ R CMD INSTALL MyPackage/ r -lMyPackage -e'print(someFunction())'
Dirk
--
Three out of two people have difficulties with fractions.
__
R-help@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.
Re: [R] What is the most efficient practice to develop an R package?
On Mon, Oct 26, 2009 at 11:22 AM, Dirk Eddelbuettel e...@debian.org wrote:
On 26 October 2009 at 07:57, Martin Morgan wrote:
| Peng Yu wrote:
| I am reading Section 5 and 6 of
| http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf
|
| It seems that I have to do the following two steps in order to make an
| R package. But when I am testing these package, these two steps will
| run many times, which may take a lot of time. So when I still develop
| the package, shall I always source('linmod.R') to test it. Once the
| code in linmod.R is finalized, then I run the following two steps?
|
| I'm wondering what people usually do when developing packages.
|
|
| 1. Run the following command in R to create the package
| package.skeleton(name=linmod, code_files=linmod.R)
|
| Do this once, to get a skeleton. Then edit the R source etc in the
| created package.
|
| 2. Run the following command in shell to install
| R CMD INSTALL -l /path/to/library linmod
|
| see R CMD INSTALL --help and use options that minimize the amount of
| non-essential work, e.g., no vignettes or documentation until that is
| the focus of your development, or --libs-only if you are working on C
| code. Use --clean to avoid stale package components. Develop individual
| functions interactively, but write a script
|
| library(MyPackage)
| someFunction()
|
| so that R -f myscript.R allows you to easily load your package and test
| specific functionality in a clean R session.
With littler you can do without the one-off script as
$ r -lMyPackage -e'print(someFunction())'
runs both commands you would have put into script. Hence, I often do
something like
$ R CMD INSTALL MyPackage/ r -lMyPackage -e'print(someFunction())'
What does the small case 'r' do?
__
R-help@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.
Re: [R] What is the most efficient practice to develop an R package?
On 26 October 2009 at 13:29, Peng Yu wrote:
| On Mon, Oct 26, 2009 at 11:22 AM, Dirk Eddelbuettel e...@debian.org wrote:
|
| On 26 October 2009 at 07:57, Martin Morgan wrote:
| | Peng Yu wrote:
| | I am reading Section 5 and 6 of
| | http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf
| |
| | It seems that I have to do the following two steps in order to make an
| | R package. But when I am testing these package, these two steps will
| | run many times, which may take a lot of time. So when I still develop
| | the package, shall I always source('linmod.R') to test it. Once the
| | code in linmod.R is finalized, then I run the following two steps?
| |
| | I'm wondering what people usually do when developing packages.
| |
| |
| | 1. Run the following command in R to create the package
| | package.skeleton(name=linmod, code_files=linmod.R)
| |
| | Do this once, to get a skeleton. Then edit the R source etc in the
| | created package.
| |
| | 2. Run the following command in shell to install
| | R CMD INSTALL -l /path/to/library linmod
| |
| | see R CMD INSTALL --help and use options that minimize the amount of
| | non-essential work, e.g., no vignettes or documentation until that is
| | the focus of your development, or --libs-only if you are working on C
| | code. Use --clean to avoid stale package components. Develop individual
| | functions interactively, but write a script
| |
| | library(MyPackage)
| | someFunction()
| |
| | so that R -f myscript.R allows you to easily load your package and test
| | specific functionality in a clean R session.
|
| With littler you can do without the one-off script as
|
| $ r -lMyPackage -e'print(someFunction())'
|
| runs both commands you would have put into script. Hence, I often do
| something like
|
| $ R CMD INSTALL MyPackage/ r -lMyPackage -e'print(someFunction())'
|
| What does the small case 'r' do?
It is a scripting front-end to R and useful for e.g. writing scripts with a
so-called shebang line (i.e #!/usr/bin/r in the first line), or for quickly
evaluating command-line expression as I showed you here, or running R scripts
instead of calling R followed by source() --- see the web page at
http://dirk.eddelbuettel.com/code/littler.html
for more.
Litter (aka 'r') is similar to Rscript which came a few months later, starts
a little slower but runs on more platforms.
Dirk
--
Three out of two people have difficulties with fractions.
__
R-help@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.
Re: [R] What is the most efficient practice to develop an R package?
Dirk Eddelbuettel wrote:
On 26 October 2009 at 13:29, Peng Yu wrote:
| On Mon, Oct 26, 2009 at 11:22 AM, Dirk Eddelbuettel e...@debian.org wrote:
|
| On 26 October 2009 at 07:57, Martin Morgan wrote:
| | Peng Yu wrote:
| | I am reading Section 5 and 6 of
| | http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf
| |
| | It seems that I have to do the following two steps in order to make an
| | R package. But when I am testing these package, these two steps will
| | run many times, which may take a lot of time. So when I still develop
| | the package, shall I always source('linmod.R') to test it. Once the
| | code in linmod.R is finalized, then I run the following two steps?
| |
| | I'm wondering what people usually do when developing packages.
| |
| |
| | 1. Run the following command in R to create the package
| | package.skeleton(name=linmod, code_files=linmod.R)
| |
| | Do this once, to get a skeleton. Then edit the R source etc in the
| | created package.
| |
| | 2. Run the following command in shell to install
| | R CMD INSTALL -l /path/to/library linmod
| |
| | see R CMD INSTALL --help and use options that minimize the amount of
| | non-essential work, e.g., no vignettes or documentation until that is
| | the focus of your development, or --libs-only if you are working on C
| | code. Use --clean to avoid stale package components. Develop individual
| | functions interactively, but write a script
| |
| | library(MyPackage)
| | someFunction()
| |
| | so that R -f myscript.R allows you to easily load your package and test
| | specific functionality in a clean R session.
|
| With littler you can do without the one-off script as
|
| $ r -lMyPackage -e'print(someFunction())'
|
| runs both commands you would have put into script. Hence, I often do
| something like
|
| $ R CMD INSTALL MyPackage/ r -lMyPackage -e'print(someFunction())'
|
| What does the small case 'r' do?
It is a scripting front-end to R and useful for e.g. writing scripts with a
so-called shebang line (i.e #!/usr/bin/r in the first line), or for quickly
evaluating command-line expression as I showed you here, or running R scripts
instead of calling R followed by source() --- see the web page at
http://dirk.eddelbuettel.com/code/littler.html
for more.
Litter (aka 'r') is similar to Rscript which came a few months later, starts
a little slower but runs on more platforms.
and for the record
R -e library(MyPackage); someFunction()
though probably a better practice is to add --vanilla (or --quiet or
--slave) too.
Martin
Dirk
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
__
R-help@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.
