[R] The steps of building library in R 2.1.1

Gabor Grothendieck ggrothendieck at gmail.com
Thu Jul 21 18:03:46 CEST 2005 

On 7/21/05, Duncan Murdoch <murdoch at stats.uwo.ca> wrote:
> On 7/21/2005 9:43 AM, Gabor Grothendieck wrote:
> > I think you have been using R too long.  Something like
> > this is very much needed.  There are two problems:
> >
> > 1. the process itself is too complex (need to get rid of perl,
> >     integrate package development tools with package installation
> >    procedure [it should be as easy as downloading a package],
> >    remove necessity to set or modify any environment variables
> >     including the path variables).
> 
> I agree with some of this, but I don't see much interest in fixing it.
> 
> For example, getting rid of Perl would be a lot of work.  When the Perl
> scripts were written, R was not capable of doing what they do.  I think
> it is capable now, but there's still a huge amount of translation work
> to do.  Who will do that?  Who will test that they did it right?  At the
> end, will it actually have been worth all the trouble?  Installing Perl
> is not all that hard.

Each step may not be hard but the totality of them all means its
pretty complex for most people.  I don't know who will do it or
whether anyone even will but a first step is identifying that it needs
to be done.  Since the key to expanding R is to expand the library
to me making it simple to create and install packages and R ought
to be of very high priority for the core group regardless of difficulty
in achieving this.  If no one is interested in doing it then it will remain
a limitation of R that commercial or other free systems can use to
gain advantage over R.

> 
> > 2. there is too much material to absorb just to create a package.
> >     The manuals are insufficient.
> 
> The first sentence here is basically a repetition of "the process is too
> complex".  I think the second sentence is incorrect.  Could you please
> point out what necessary steps are missing?

Its not that anything is missing that I am aware of.  Its that there is so much 
detail one is overwhelmed.  Its not completely the fault of the description 
since as point #1 mentions the process itself is a key part of the 
problem.

> >
> > A step-by-step simplification is very much needed.
> 
> Exactly this has been in the Installation and Administration manual
> since I put it there in February for the 2.1.0 release.  It's at the
> beginning of the appendix on the Windows toolset, with multiple
> references pointing people there.  It's followed by detailed
> descriptions of each of the steps.
> 
> If you think it could be further improved, please submit improvements.

That is easy to say but, in fact, if anyone does this they are not met
with a receptive atmosphere.  The excellent post describing the process
that started this out (even if there are some small errors) is just one 
example.  

> 
>  >Its no
> > coincidence that there are a number of such descriptions on
> > the net (google for 'making creating R package') since I would
> > guess that just about everyone has significant problems in creating
> > their first package on Windows.
> 
> As far as I can tell, those all predate the release of 2.1.0.  I think
> your complaints are out of date.

I am sure the situation is getting better but I did look at the manuals
again before posting and do think that a step by step article such
as that in Ivy Li's post, the various documents on the net findable by google
as I mentioned and the proposed article by Uwe are really needed
in addition to the manuals.  The manuals can then be used to get
additional detail.

> 
> Duncan Murdoch
> 
> >
> >
> > On 7/21/05, Uwe Ligges <ligges at statistik.uni-dortmund.de> wrote:
> >> Ivy_Li wrote:
> >>
> >> > Dear All,
> >> >
> >> > With the warm support of every R expert, I have built my R library successfully.
> >> > Especially thanks: Duncan Murdoch
> >> >                   Gabor Grothendieck
> >> >                   Henrik Bengtsson
> >> >                   Uwe Ligges
> >>
> >> You are welcome.
> >>
> >>
> >> The following is intended for the records in the archive in order to
> >> protect readers.
> >>
> >>
> >> > Without your help, I will lower efficiency.
> >> > I noticed that some other friends were puzzled by the method of building library. Now, I organize a document about it. Hoping it can help more friends.
> >> >
> >> > 1. Read the webpage <http://www.stats.ox.ac.uk/pub/Rtools>
> >>
> >> Do you mean http://www.murdoch-sutherland.com/Rtools/ ?
> >>
> >> > 2. Download the "rw2011.exe"; Install the newest version of R
> >> > 3. Download the "tools.zip"; Unpack it into c:\cygwin
> >>
> >> Not required to call it "cygwin" - also a bit misleading...
> >>
> >> > 4. Download the "ActivePerl-5.6.1.633-MSWin32-x86.msi"; Install Active Perl in c:\Perl
> >>
> >> Why in C:\Perl ?
> >>
> >> > 5. Download the "MinGW-3.1.0-1.exe"; Install the mingw32 port of gcc in c:\mingwin
> >>
> >> Why in c:\mingwin ?
> >>
> >>
> >> > 6. Then go to "Control Panel -> System -> Advanced -> Environment Variables -> Path -> Variable Balue"; add "c:\cygwin;c:\mingwin\bin"
> >> >       The PATH variable already contains a couple of paths, add the two given above in front of all others, separated by ";".
> >> >       Why we add them in the beginning of the path? Because we want the folder that contains the tools to be at the beginning so that you eliminate the possibility of finding a different program of the same name first in a folder that comes prior to the one where the tools are stored.
> >>
> >>
> >> OK, this (1-6) is all described in the R Administration and Installation
> >> manual, hence I do not see why we have to repeat it here.
> >>
> >>
> >> > 7. I use the package.skeleton() function to make a draft package. It will automate some of the setup for a new source package. It creates directories, saves functions and    data to appropriate places, and creates skeleton help files and 'README' files describing further steps in packaging.
> >> > I type in R:
> >> >       >f <- function(x,y) x+y
> >> >       >g <- function(x,y) x-y
> >> >       >d <- data.frame(a=1, b=2)
> >> >       >e <- rnorm(1000)
> >> >       >package.skeleton(list=c("f","g","d","e"), name="example")
> >> > Then modify the 'DESCRIPTION':
> >> >       Package: example
> >> >       Version: 1.0-1
> >> >       Date: 2005-07-09
> >> >       Title: My first function
> >> >       Author: Ivy <Ivy_Li at smics.com>
> >> >       Maintainer: Ivy <Ivy_Li at smics.com>
> >> >       Description: simple sum and subtract
> >> >       License: GPL version 2 or later
> >> >       Depends: R (>= 1.9), stats, graphics, utils
> >> > You can refer to the web page: http://cran.r-project.org/src/contrib/Descriptions/  There are larger source of examples. And you can read the part of 'Creating R Packages' in 'Writing R Extension'. It introduces some useful things for your reference.
> >>
> >>
> >> This is described in Writing R Extension and is not related to the setup
> >> of you system in 1-6.
> >>
> >>
> >> >
> >> > 8. Download hhc.exe Microsoft help compiler from somewhere. And save it somewhere in your path.
> >> >     I download a 'htmlhelp.exe' and setup. saved the hhc.exe into the 'C:\cygwin\bin' because this path has been writen in my PATH Variable Balue.
> >> >     However if you decided not to use the Help Compiler (hhc), then you need to modify the MkRules file in RHOME/src/gnuwin32 to tell it not to try to build that kind of help file
> >>
> >>
> >> This is described in the R Administration and Installation manual
> >> and I do not see why we should put the html compiler to the other tools.
> >>
> >>
> >> > 9. In the DOS environment. Into the "D:\>"  Type the following code:
> >>
> >> There is no DOS environment in Windows NT based operating systems.
> >>
> >>
> >> >       cd \Program Files\R\rw2010
> >> >       bin\R CMD INSTALL "/Program Files/R/rw2011/example"
> >>
> >> I do not see why anybody would like to contaminate the binary
> >> installation of R with some development source packages.
> >> I'd rather use a separate directory.
> >>
> >> I think reading the two mentioned manuals shoul be sufficient. You have
> >> not added relevant information. By adding irrelevant information and
> >> omitting some relevant information, I guess we got something that is
> >> misleading if the reader does NOT read the manuals as well.
> >>
> >> Best,
> >> Uwe Ligges
> >>
> >>
> >> > Firstly, because I install the new version R in the D:\Program Files\. So I should first into the D drive. Secondly, because I use the package.skeleton() function to build 'example' package in the path of D:\Program Files\R\rw2011\  So I must tell R the path where saved the 'example' package. So I write the code is like that. If your path is different from me, you should modify part of these code.
> >> >
> >> > 10.Finally, this package is successfully built up.
> >> >
> >> >         ---------- Making package example ------------
> >> >         adding build stamp to DESCRIPTION
> >> >         installing R files
> >> >         installing data files
> >> >         installing man source files
> >> >         installing indices
> >> >         not zipping data
> >> >         installing help
> >> >        >>> Building/Updating help pages for package 'example'
> >> >            Formats: text html latex example chm
> >> >         d                                 text    html    latex   example
> >> >         e                                 text    html    latex   example
> >> >         f                                 text    html    latex   example
> >> >         g                                 text    html    latex   example
> >> >         adding MD5 sums
> >> >
> >> >       * DONE (example)
> >> >
> >> > I was very happy to get the great results. I hope the document can help you. Thank you again for everyone's support.
> >> >
> >> >
> >> > Best Regards!
> >> > Ivy Li£¨Àîè¡£©
> >> > YMS in Production & Testing
> >> > Semiconductor Manufactory International(ShangHai) Corporation
> >> > #18 ZhangJiang Road, PuDong New Area, Shanghai, China
> >> > Tel: 021-5080-2000 *11754
> >> > Email: Ivy_Li at smics.com
> >> >
> >> >
> >> >
> >> > ------------------------------------------------------------------------
> >> >
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> >> > https://stat.ethz.ch/mailman/listinfo/r-help
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> >>
> >>
> >>
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> >>
> >
> >
> > ------------------------------------------------------------------------
> >
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