Re: [R] [SPAM] - Re: R package development in windows - Bayesian Filter detected spam

From: Gabor Grothendieck <ggrothendieck_at_gmail.com>
Date: Fri, 04 May 2007 10:19:43 -0400

I was able to click the link in your reply and it worked so there is some problem with your email viewer. You can google for:

    code google batchfiles

and use the first hit or type the URL in by hand.

On 5/4/07, Doran, Harold <HDoran_at_air.org> wrote:
> Hi Gabor:
>
> I tried the link below, but it seems to be broken.
>
> > -----Original Message-----
> > From: Gabor Grothendieck [mailto:ggrothendieck_at_gmail.com]
> > Sent: Friday, May 04, 2007 10:05 AM
> > To: Doran, Harold
> > Cc: Duncan Murdoch; r-help_at_stat.math.ethz.ch
> > Subject: [SPAM] - Re: [R] R package development in windows -
> > Bayesian Filter detected spam
> >
> > Regarding your comments on changing paths,
> >
> > 1. Rcmd.bat in the batchfiles distribution
> >
> > http://code.google.com/p/batchfiles/
> >
> > can be used to avoid having to change the path (other than
> > path changes required for perl and tex which you would
> > probably want anyways to be able to use those). You will
> > only have to place Rcmd.bat, hhc.exe and the tools somewhere
> > in your existing path. I keep a \bin directory in my path
> > for that purpose. It also allows you to avoid having to
> > change paths when you install a new version of R.
> >
> > Also in the batchfiles distribution is Rfind.bat that will
> > search your system and try to find the various tools on it.
> > Its display only so it should be safe to use and can help you
> > determine if something is missing and where various tools are
> > on your machine.
> >
> > 2. Also did you follow up on my suggestions? There are TWO
> > relevant links in the Links section of the batchfiles home page
> >
> > http://code.google.com/p/batchfiles/
> >
> > as I mentioned in my prior emails:
> >
> > HowTo: Create an R Package
> > HowTo: Create an R Package (manuals)
> >
> > The first gives step by step instructions and the second is a
> > link to the authoritative source, the manuals and BOTH of
> > them should be read, not just the manuals.
> >
> >
> > On 5/4/07, Doran, Harold <HDoran_at_air.org> wrote:
> > > OK, so I just want to go on record as noting that following the
> > > instructions exactly (exactly, exactly, exactly,
> > emphatically) on the
> > > web given by Duncan, Gabor, and Tony at the page below, and
> > following
> > > the instructions in Writing R Extensions results in a successful
> > > Windows build of a package.
> > >
> > > Should this email turn up in someones search using RSiteSearch() or
> > > elsewhere, my best advice is to ignore all other documents
> > on the web
> > > attempting to explain this. I personally went through 4 or
> > 5 different
> > > personal web sites looking for a straightforward guide.
> > After a week
> > > or so of late night reading and experimentation, all of those
> > > documents led me to a path of failure. After reading the
> > info on the
> > > link below, and then referring back to Writing R Extensions, I was
> > > able to build the package in only a few hours of time. It took
> > > significantly less time to read the manual and information
> > on the link
> > > below than it did to google help pages on the topic, read
> > those, and end up even more confused.
> > >
> > > I'm not in the best position to offer specific
> > recommendations on how
> > > to improve this process. The reality is that after collecting all
> > > programs required, making the required changes to the path,
> > the Rcmd
> > > commands for the build are very simple. So, the biggest task is the
> > > collection of essential programs and modification to the path.
> > >
> > > Obviously, Rtools is designed to move forward in this
> > direction. Its
> > > current phase still doesn't automate that collection and
> > modification
> > > process entirely, and the reasons are given on Duncan's web site.
> > > However, I suppose the only good recommendation I can make at this
> > > point is to still move forward with Rtools such that it
> > installs all
> > > required programs and automatically updates the path accordingly.

> > > Maybe this can even become part of the base installation. Since the
> > > open source nature of R encourages development, the tools
> > needed for
> > > development should be readily available.
> > >
> > > I am certain this recommendation is not novel, and Duncan
> > et al have
> > > already thought of this. But, it's my attempt to do a little better
> > > than complain.
> > >
> > > The only other piece of advice I can offer is to keep this stable.
> > > That is, when R 2.5.1 et seq are released, I beg of the
> > developers not
> > > to require a new collection of tools or a different set up
> > than what
> > > is already required. It is a bit of work, and if changes
> > are required
> > > at each R release, this may be too disheartening.
> > >
> > > Harold
> > >
> > > > -----Original Message-----
> > > > From: Duncan Murdoch [mailto:murdoch_at_stats.uwo.ca]
> > > > Sent: Thursday, May 03, 2007 3:51 PM
> > > > To: Doran, Harold
> > > > Cc: Gabor Grothendieck; r-help_at_stat.math.ethz.ch
> > > > Subject: [SPAM] - Re: [SPAM] - Re: [R] R package development in
> > > > windows - Bayesian Filter detected spam - Bayesian Filter
> > detected
> > > > spam
> > > >
> > > > On 5/3/2007 3:33 PM, Doran, Harold wrote:
> > > > > Thanks, Duncan. I'll look into that. Is there an authoritative
> > > > > document that codifies the new package development
> > procedures for
> > > > > 2.5.0 (windows-specific), or is that Writing R
> > Extensions? In this
> > > > > thread alone I've received multiple emails pointing to multiple
> > > > > web sites with instructions for windows. Inasmuch as its
> > > > appreciated, I'm
> > > > > a bit confused as to which I should consider authoritative.
> > > > >
> > > > > I do hope I can resolve this and appreciate the help
> > I've received.
> > > > > However, I feel a bit compelled to note how very difficult this
> > > > > process is.
> > > >
> > > > The manuals are the authoritative reference. Writing R
> > Extensions
> > > > tells you what to do to set up a package. The R
> > Administration and
> > > > Installation manual tells you how to set up your system so those
> > > > instructions will work. On Windows, you want to pay particular
> > > > attention to the appendix of the Admin manual called "The Windows
> > > > Toolset". This is Appendix E in the distributed .pdf; an HTML
> > > > version is available here:
> > > >
> > > >
> > > >
> > http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-tools
> > > > et
> > > >
> > > > We realize that these instructions are not easy to
> > follow, there's
> > > > no need to tell us that. However, specific corrections or
> > > > improvements would be welcome.
> > > >
> > > > Duncan Murdoch
> > > >
> > > >
> > > > > Harold
> > > > >
> > > > >
> > > > >> -----Original Message-----
> > > > >> From: Duncan Murdoch [mailto:murdoch_at_stats.uwo.ca]
> > > > >> Sent: Thursday, May 03, 2007 3:24 PM
> > > > >> To: Doran, Harold
> > > > >> Cc: Gabor Grothendieck; r-help_at_stat.math.ethz.ch
> > > > >> Subject: [SPAM] - Re: [R] R package development in windows
> > > > - Bayesian
> > > > >> Filter detected spam
> > > > >>
> > > > >> On 5/3/2007 3:04 PM, Doran, Harold wrote:
> > > > >> > Thanks Gabor, Sundar, and Tony. Indeed, Rtools was
> > > > missing from the
> > > > >> > path. With that resolved, and another 10 minute windows
> > > > >> restart, I get
> > > > >> > the following below. The log suggests that hhc is not
> > > > installed. It
> > > > >> > is, and, according to the directions I am following, I have
> > > > >> placed it
> > > > >> > in the c:\cygwin directory.
> > > > >>
> > > > >> I think the problem is that you are following a real mix of
> > > > >> instructions, and they don't make sense.
> > > > >>
> > > > >> It would be nice if folks would submit patches to the R
> > > > Admin manual
> > > > >> (or to the Rtools web site) rather than putting together web
> > > > >> sites with advice that is bad from day one, and quickly gets
> > > > worse when it
> > > > >> is not updated.
> > > > >>
> > > > >> > BTW, package.skeleton() doesn't seem to create the correct
> > > > >> DESCRIPTION
> > > > >> > template. I had to add the DEPENDS line. Without this, I
> > > > >> get another
> > > > >> > error.
> > > > >> >
> > > > >> >
> > > > >> > C:\Program Files\R\R-2.4.1\bin>Rcmd build --force --binary
> > > > >> > g:\foo
> > > > >>
> > > > >> R 2.4.1 is no longer current; the package building
> > > > instructions in R
> > > > >> 2.5.0 have been simplified a bit. You might want to try those.
> > > > >>
> > > > >> Duncan Murdoch
> > > > >>
> > > > >> > * checking for file 'g:\foo/DESCRIPTION' ... OK
> > > > >> > * preparing 'g:\foo':
> > > > >> > * checking DESCRIPTION meta-information ... OK
> > > > >> > * removing junk files
> > > > >> > * checking for LF line-endings in source files
> > > > >> > * checking for empty or unneeded directories
> > > > >> > * building binary distribution
> > > > >> > WARNING
> > > > >> > * some HTML links may not be found installing R.css in
> > > > >> > c:/TEMP/Rinst40061099
> > > > >> >
> > > > >> > Using auto-selected zip options ''
> > > > >> > latex: not found
> > > > >> > latex: not found
> > > > >> > latex: not found
> > > > >> >
> > > > >> > ---------- Making package foo ------------
> > > > >> > latex: not found
> > > > >> > adding build stamp to DESCRIPTION
> > > > >> > latex: not found
> > > > >> > latex: not found
> > > > >> > latex: not found
> > > > >> > installing R files
> > > > >> > latex: not found
> > > > >> > installing data files
> > > > >> > latex: not found
> > > > >> > installing man source files
> > > > >> > installing indices
> > > > >> > latex: not found
> > > > >> > not zipping data
> > > > >> > installing help
> > > > >> > Warning: \alias{foo} already in foo-package.Rd -- skipping
> > > > >> the one in
> > > > >> > foo.Rd >>> Building/Updating help pages for package 'foo'
> > > > >> > Formats: text html latex example chm
> > > > >> > foo-package text html latex
> > > > >> example chm
> > > > >> > foo text html latex
> > > > >> example chm
> > > > >> > mydata text html latex
> > > > >> example chm
> > > > >> > hhc: not found
> > > > >> > cp: cannot stat `c:/TEMP/Rbuild40048815/foo/chm/foo.chm':
> > > > >> No such file
> > > > >> > or direct ory
> > > > >> > make[1]: *** [chm-foo] Error 1
> > > > >> > make: *** [pkg-foo] Error 2
> > > > >> > *** Installation of foo failed ***
> > > > >> >
> > > > >> > Removing 'c:/TEMP/Rinst40061099/foo'
> > > > >> > ERROR
> > > > >> > * installation failed
> > > > >> >
> > > > >> >
> > > > >> > C:\Program Files\R\R-2.4.1\bin>
> > > > >> >
> > > > >> >> -----Original Message-----
> > > > >> >> From: Gabor Grothendieck [mailto:ggrothendieck_at_gmail.com]
> > > > >> >> Sent: Thursday, May 03, 2007 2:50 PM
> > > > >> >> To: Doran, Harold
> > > > >> >> Cc: r-help_at_stat.math.ethz.ch
> > > > >> >> Subject: Re: [R] R package development in windows
> > > > >> >>
> > > > >> >> It can find sh.exe so you haven't installed Rtools.
> > > > >> >>
> > > > >> >> There are several HowTo's listed in the links section here
> > > > >> >> that include pointers to R manuals and other step by step
> > > > >> >> instructions:
> > > > >> >>
> > > > >> >> http://code.google.com/p/batchfiles/
> > > > >> >>
> > > > >> >> On 5/3/07, Doran, Harold <HDoran_at_air.org> wrote:
> > > > >> >> > I'm attempting to build an R package for distribution and
> > > > >> >> am working
> > > > >> >> > from the directions found at
> > > > >> >> >
> > > > >> >>
> > > > >>
> > > >
> > http://www.maths.bris.ac.uk/~maman/computerstuff/Rhelp/Rpackages.htm
> > > > l
> > > > >> >> #
> > > > >> >> > Wi
> > > > >> >> > n-Win
> > > > >> >> >
> > > > >> >> > I've read through Writing R Extensions and various other
> > > > >> >> "helpful" web
> > > > >> >> > sites. I've installed all relevant software (perl,
> > > > >> cygwin, mingwin,
> > > > >> >> > hhc.exe). Here is what I have done so far:
> > > > >> >> >
> > > > >> >> > 1) Sourced data and functions into R
> > > > >> >> > 2) Used package.skeleton
> > > > >> >> > 3) Edited Description file
> > > > >> >> > 4) Edited my windows path to ensure the new
> > programs (e.g.,
> > > > >> >> perl) are
> > > > >> >> > in the path
> > > > >> >> > 5) Then, I open DOS and do the following in the
> > script below
> > > > >> >> >
> > > > >> >> > C:\Program Files\R\R-2.4.1\bin>Rcmd build --force
> > > > >> --binary g:\foo
> > > > >> >> > * checking for file 'g:\foo/DESCRIPTION' ... OK
> > > > >> >> > * preparing 'g:\foo':
> > > > >> >> > * checking DESCRIPTION meta-information ...'sh' is not
> > > > >> >> recognized as
> > > > >> >> > an internal or external command, operable program or
> > > > batch file.
> > > > >> >> > OK
> > > > >> >> > * removing junk files
> > > > >> >> > 'sh' is not recognized as an internal or external
> > > > >> command, operable
> > > > >> >> > program or batch file.
> > > > >> >> > 'sh' is not recognized as an internal or external
> > > > >> command, operable
> > > > >> >> > program or batch file.
> > > > >> >> > 'sh' is not recognized as an internal or external
> > > > >> command, operable
> > > > >> >> > program or batch file.
> > > > >> >> > Error: cannot open file 'foo/DESCRIPTION' for reading
> > > > >> >> >
> > > > >> >> > I'ver read through about as much documentation as I can
> > > > >> >> find, and I'm
> > > > >> >> > just not sure what I should do from here. I admit that I
> > > > >> >> have reached
> > > > >> >> > a point of frustration and must apologize if the problem
> > > > >> would be
> > > > >> >> > evident if I read documentation further, but I'm about
> > > > >> tapped out
> > > > >> >> > after a few days of experimentation.
> > > > >> >> >
> > > > >> >> > Can anyone suggest how I could resolve this and what the
> > > > >> next steps
> > > > >> >> > would be?
> > > > >> >> >
> > > > >> >> > Thanks:
> > > > >> >> >
> > > > >> >> > I'm using Windows XP and R 2.4.1
> > > > >> >> >
> > > > >> >> > Harold
> > > > >> >> >
> > > > >> >> > [[alternative HTML version deleted]]
> > > > >> >> >
> > > > >> >> > ______________________________________________
> > > > >> >> > R-help_at_stat.math.ethz.ch 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.
> > > > >> >> >
> > > > >> >>
> > > > >> >
> > > > >> > ______________________________________________
> > > > >> > R-help_at_stat.math.ethz.ch 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.
> > > > >>
> > > > >>
> > > >
> > > >
> > >
> >
>



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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. Received on Fri 04 May 2007 - 14:49:36 GMT

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