From andy_liaw at merck.com  Thu Nov 11 19:31:23 2004
From: andy_liaw at merck.com (Liaw, Andy)
Date: Thu Nov 11 19:32:12 2004
Subject: [Rd] Questions on package creation
Message-ID: <3A822319EB35174CA3714066D590DCD50994E2D7@usrymx25.merck.com>

I write most of the code in randomForest in Windows, and move to Linux when
I need to debug compiled code.  On my WinXPPro laptop, I have a directory
c:/home/R-packages/RF.  That's where the randomForest source tree lives.
When I'm ready to do some test, I would do (on the command line, in
c:/home/R-packages/RF)

  mkdir test
  R CMD INSTALL -l test randomForest

If the install is OK, I then start up Rterm or Rgui from the directory and
do

  library(randomForest, lib.loc="test")

and play with the package a bit to make sure it looks OK.  Then at the
system command line,

  R CMD check randomForest

If that goes well, I'd do:

  R CMD build --force randomForest
  R CMD build --binary randomForest

and move the .tar.gz and .zip archives to whereever I want them.  Before I
use subversion for version control, I would simply stash away the .tar.gz in
c:/home/R-packages/rf-pkg, which holds the tarball of various versions of
the package.  Not particularly efficient, obviously.

HTH,
Andy
  

> From: Gabor Grothendieck
> 
> Thanks.  One thing I would like clarified is the various locations
> and what is relative to where.
> 
> If you could add to the example where we are in terms of an example
> absolute path and where the various directories wind up also in
> terms of example absolute paths it would clear up a lot.
> 
> Liaw, Andy <andy_liaw <at> merck.com> writes:
> 
> : 
> : Gabor,
> : 
> : Here are my takes on these:
> : 
> : 1: Not that I know of.  Only the package developer(s) see 
> the code this way,
> : and is really not different from 3.  (A developer would not 
> need 3, as R CMD
> : check can be done with 1.)
> : 
> : 2 & 4: As Uwe said, the location is `whereever you like'.  
> You would create
> : them only for distribution (i.e., installation on other 
> machines), so it
> : doesn't matter where it put them.  They only exist 
> temporarily on the
> : developer's machine (assuming the source is version 
> controlled via other
> : means), as only a user wanting to install the package would 
> need the archive
> : forms.
> : 
> : Here's the sequence I use:
> : 
> : Start with a source tree for the package somewhere.
> : 
> : Testing/checking:
> : 
> : Run R CMD INSTALL -l mytest mypkg (making sure you create 
> the `mytest'
> : directory first).  This installs the package in the 
> `mytest' directory.  If
> : the install is not successful, make necessary changes.  If 
> successful, start
> : up R (from the command line) and do library(mypkg, 
> lib.loc="mytest") and run
> : some tests (e.g., example() for functions in the package).
> : 
> : After making sure the installed package looks good, run R 
> CMD check mypkg.
> : Make changes to correct errors and warnings.
> : 
> : After successful check, run R CMD build --force mypkg to 
> generate the source
> : tarball and update the INDEX file.  (The --force is only 
> needed if you
> : add/remove/change help page topics since the last build.)
> : 
> : Run R CMD build --binary mypkg if you need to distribute 
> the package in
> : binary form.
> : 
> : HTH,
> : Andy
> : 
> : > From: Gabor Grothendieck
> : > 
> : > I have some questions about 
> : > 
> : >    1. nomenclature, 
> : >    2. recommended file locations and 
> : >    3. overall procedure related to creating packages.
> : > 
> : > To the extent that it matters, examples here relate to Windows XP
> : > R 2.0.1 beta.  
> : > 
> : > The questions are interspersed and prefaced with ***.
> : > 
> : > My understanding is that there are actually 6 forms of a package
> : > that one should use in package development:
> : > 
> : > 1. original package.  This refers to the original source files, 
> : >    documentation and other files that the author develops.  
> : >    If source control, e.g. svn, is used then these are the files 
> : >    that are under source control.  They are kept in some 
> arbitrary 
> : >    location on one's disk.  Let us say \usr\mypackage, 
> for example.
> : > 
> : > *** Is there some standard name for this form of the package?
> : > 
> : > 2. source archive.  This is created from the original package
> : >    like this:
> : > 
> : >      cd \Program Files\rw2001beta
> : >      bin\R CMD build /usr/mypackage
> : > 
> : >    which creates, say
> : > 
> : >      \Program Files\rw2001beta\mypackage_1.0-1.tar.gz
> : > 
> : >    The source archive is distinct from the original 
> archive since it
> : >    is specific to a version of R and excludes the files referenced
> : >    in \usr\mypackage\.Rbuildignore
> : > 
> : > *** Is \Program Files\rw2001beta the correct place to put this
> : >    .tar.gz file?
> : > 
> : > 3. source tree.  This is created from the gzipped tar 
> archive in #2
> : >    like this:
> : > 
> : >      cd \Program Files\rw2001beta
> : >      gzip -d mypackage_1.0-1.tar.gz
> : >      cd src\library
> : >      tar xvf ..\..\mypackage_1.0-1.tar
> : > 
> : >    and is checked like this:
> : > 
> : >      cd \Program Files\rw2001beta
> : >      bin\R CMD check mypackage
> : > 
> : > 4. binary archive.  This is created from the source archive in #2
> : >    or the source tree in #3:
> : > 
> : >       cd \Program Files\rw2001beta
> : >       bin\R CMD build mypackage --binary
> : >     
> : >    which creates \Program Files\rw2001beta\myhpackage_1.0-1.zip
> : > 
> : > *** Is \Program Files\rw2001beta the correct place to put this?
> : > 
> : > 5. installed package.  This installed by:
> : > 
> : >      cd \Program Files\rw2001beta
> : >      bin\R CMD install mypackage
> : > 
> : >   which results in the source package being installed in:
> : >   
> : >      \Program Files\rw2001beta\library\mypackage
> : > 
> : >   This can alternately be done with the R GUI menu: 
> : > 
> : >     Packages | Install package(s) from local zip files
> : > 
> : > 6. loaded package.  In R using the command:
> : > 
> : >      library(mypackage)
> : > 
> : >    loads the package into R.  This can alternately be done
> : >    using the R GUI menu:
> : > 
> : >       Packages | Load package
> : > 
> : > One might initially skip #3 and #4 and just test the package out
> : > in R after #6 and once one is satisfied that it is in good shape
> : > repeat the sequence.
> : > 
> : > *** Is all the above the correct and recommended sequence?
> : > 
> : > *** Someone mentioned that --force is important.  How does that 
> : >     fit into all this?  I still have not used it and am not sure
> : >     about it.
> : > 
> : > ______________________________________________
> : > R-devel <at> stat.math.ethz.ch mailing list
> : > https://stat.ethz.ch/mailman/listinfo/r-devel
> : > 
> : >
> : 
> : ______________________________________________
> : R-devel <at> stat.math.ethz.ch mailing list
> : https://stat.ethz.ch/mailman/listinfo/r-devel
> : 
> :
> 
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
>


[Rd] Questions on package creation
Liaw, Andy