Re: [R] R package development in windows

From: Gabor Grothendieck <ggrothendieck_at_gmail.com>
Date: Fri, 04 May 2007 13:48:15 -0400

On 5/4/07, Duncan Murdoch <murdoch_at_stats.uwo.ca> wrote:
> On 5/4/2007 11:31 AM, Gabor Grothendieck wrote:
> > On 5/4/07, Duncan Murdoch <murdoch_at_stats.uwo.ca> wrote:
> >> On 5/4/2007 9:30 AM, Doran, Harold 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.
> >>
> >> Thanks for your comments and suggestions. I've thought of a few changes
> >> we can make; let me know if you see any problems with these:
> >>
> >> 1. I will simplify the Rtools site. Rather than duplicating the
> >> information from the R-admin manual, I will just include the
> >> #The-Windows-toolset link as given below, together with post-release
> >> updates. This should help with the "too many places to look" problem.
> >> Now, if other sites did the same...
> >>
> >> 2. You suggest that Rtools.exe make automatic changes to the user's
> >> PATH. I'm quite reluctant to do that, because what R needs may conflict
> >> with what a user needs for other work. However, something that I think
> >> would be fairly easy to do would be to install a shortcut to start a
> >> CMD.EXE or Cygwin shell with the path set appropriately. I'll look into
> >> that.
> >
> >
> > I agree that setting the path permanently would be bad but
> > the shortcut could check to see if they are in the path already
> > and if not it could find them in the registry and just change the
> > session path rather than permanently set the path.

>

> Do you have a batch file already to do this? If I were writing it, I'd
> do something simpler: I'd just hard code the paths, and expect the user
> to edit the file if I didn't get them right.

rfind.bat in batchfiles checks the registry for all of these but it does not set the path (although it does output a possible path you can use without actually setting it) since I wanted the command to be completely safe, i.e. display only.

C:\>path=c:\windows;c:\windows\system32

C:\>\bin\rfind
PerlDir=\perl\bin\
TeXDir=C:\texmf\miktex\bin
HTMLHelpDir=C:\Program Files\HTML Help Workshop

R_HOME=C:\Program Files\R\R-2.5.0
Rbin=C:\Program Files\R\R-2.5.0\bin
R_ROOT=C:\Program Files\R

RtoolsDir=\bin\
RPATH=C:\Program Files\R\R-2.5.0\bin;\bin\;\perl\bin\;C:\Program Files\HTML Help  Workshop;;c:\windows;c:\windows\system32
>

> >> 3. You also suggested adding more tools to Rtools.exe. I think the key
> >> tool to add would be Perl; it's the only essential tool that's currently
> >> missing. Unfortunately, there are licensing issues with that for
> >> ActiveState Perl, the version we currently recommend. I'll try to get
> >> specific permission from ActiveState to include a copy.
> >>
> >
> > The best, of course, would be to get rid of Perl altogether.

>

> I agree, but there is a lot of Perl code in the R scripts now, and I
> think the maintainers of those scripts are comfortable with it. I think
> R code for string handling is even harder to read than Perl, so it's not
> likely to change.
>

> >> 4. We could include the tools in the base installation of R; that's
> >> what the MacOSX release has done. However, that would at least double
> >> the size of the download, even with just the minimal additions, and
> >> under the GPL would require CRAN and its mirrors to host source for most
> >> of the tools. What I plan to do instead is to put a link to the Rtools
> >> page on the CRAN page for the Windows R binary.
> >
> > Some other possiblities are:
> > - use a different toolset. I seem to remember that there were a few very
> > compact toolsets for use with minimal systems. One basically put all
> > the UNIX tools in one executable and you could just rename it successively
> > to each tool you wanted. Another one used lua for implementation which
> > is embeddable and very small.
>

> This is not really relevant. The Unix command line tools are fine:
> Rtools.exe installs them, and they just work, if you get the PATH right.
> The current "problem children" are Perl, LaTeX, and HHW. (Also Inno
> Setup, but it's not for package builders).

You indicated the problem with including them is that it would make the R download twice as large so the size is the key issue, at least based on your prior comments as I understand them.

>

> > - rewrite as many tools as possible in R. The full power of the tool might
> > not be needed making it easier. If 80% of the tools could be easily eliminated
> > it might not be a problem to include the remaining 20%. Or if 20% of the
> > tools take up 80% of the space this might be sufficient. Of course getting
> > them all in R would be nice.
>

> Rewriting the Perl code as R scripts is imaginable, but rewriting LaTeX
> and HHW in R is not.

Yes, that's what I meant. I realize its not feasible to rewrite latex and the help compiler.

>

> >> 5. We could modify the MkRules file that we distribute with R to assume
> >> the minimal toolset, i.e. no LaTeX or CHM help. This would mean you'd
> >> get fewer "not found" messages from a basic install, but might be a
> >> little inconvenient for people who have the tools. Perhaps we can
> >> detect whether those tools have been installed and act accordingly.
> >>
> >
> > Not sure I understand this but could this be decided upon automatically
> > by checking the user's registry for the existence of the tools?
>

> It might be possible to automate the tests by looking at the PATH.
> Neither LaTeX nor HHW is necessarily going to show up at a predictable
> location in the registry.

I am not sure about this. rfind.bat currently uses the registry to find them. Is there anything wrong with the way it works?

>

> Duncan Murdoch
>

> >> 6. You suggested avoiding changes to the toolset. This is hard,
> >> because the updates often fix bugs in older versions. Bugs in the tools
> >> lead to bugs in R. So I think we don't have much choice but to continue
> >> to make necessary updates.
> >>
> >> Duncan Murdoch
> >>
> >>
> >> >
> >> > 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-toolset
> >> >>
> >> >> 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.html
> >> >> >> >> #
> >> >> >> >> > 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 - 17:56:24 GMT

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