Re: [Rd] I'm unable to download R from any of the CRAN mirrors. Any sugge (PR#7823)

[Friedrich . Leisch]

>>>>> On 29 Apr 2005 17:29:43 +0200,
>>>>> Peter Dalgaard (PD) wrote:

  > This is not a bug in R. Please do not misuse the bug repository.

  > The central CRAN site in Vienna was offline for some hours tonight.
  > This may have disrupted mirroring, but things look like they are back
  > to normal.

Actually if our server is down that shouldn't affect mirroring too
much (most mirroring software is smart enough not to delete everything
is the master site is unreacheable), but URLs of form

cran.XX.r-project.org

may not work because most of them do not have a DNS entry but are
apache redirections by our server. In that case simply use a CRAN
mirror with a non r-project.org address, a current list can be
obtained by running

 read.csv(file.path(R.home(), "doc", "CRAN_mirrors.csv", as.is=TRUE))[,"URL"]

in a recent version of R ... I'll encapsulate that into a
one-liner CRAN_mirrors().

-- 
-------
Friedrich Leisch 
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch

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Re: [Rd] citation() chops "Roeland " (PR#7797)

[Friedrich . Leisch]

> On 18 Apr 2005 11:18:03 +0200,
> Peter Dalgaard (PD) wrote:

  > [EMAIL PROTECTED] writes:
  >> Full_Name: Jari Oksanen
  >> Version: 2.0.1, 2.1.0 beta (2005-04-17)
  >> OS: Linux
  >> Submission from: (NULL) (130.231.102.145)
  >> 
  >> 
  >> If name ends with "and", such as "Roeland Lastname", citation() will chop 
"and"
  >> as a separate word giving "Roel and Lastname". This is the case in the 
upcoming
  >> release of vegan (1.6-8) just submitted to CRAN. Basically, this seems to 
happen
  >> in utils:::as.personList.default
  >> 
  >> > unlist(as.personList("Roeland Lastname"))
  >> name.first name.middle   name.last  name.first name.middle   name.last
  >> ""  ""  "Roel"  ""  ""  "Lastname"
  >> 
  >> and the culprit line seems to be:
  >> 
  >> x <- unlist(strsplit(x, "[[:space:]]?(,|and)[[:space:]]+"))
  >> 
  >> Fortunately, persons like Anders Andtfolk and Mandalay Grandjean are not
  >> chopped, because they don't have space after "and".

  > I'm sure it'll annoy Anders|George Sand, Bertrand Russell, Inge
  > Helland, et al., but it hardly counts as release-critical, nor trivial
  > enough to slip in during code freeze, especially as regular
  > expressions are involved (does one *ever* get them right on the first
  > try?)

Certainly not release critical ... especially as the conversion
doesn't claim to work in all cases and is there only for convenience:

person("Roeland", "Lastname")

does the right thing, so one can write a correct CITATION file.

unlist(strsplit(x, "[[:space:]]?(,|[[:space:]]and)[[:space:]]+"))


should do the trick, I'll put it into the patched branch after
release.

.f

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Re: [Rd] citation() chops "Roeland " (PR#7797)

[Friedrich . Leisch]

> On 18 Apr 2005 11:18:03 +0200,
> Peter Dalgaard (PD) wrote:

  > [EMAIL PROTECTED] writes:
  >> Full_Name: Jari Oksanen
  >> Version: 2.0.1, 2.1.0 beta (2005-04-17)
  >> OS: Linux
  >> Submission from: (NULL) (130.231.102.145)
  >> 
  >> 
  >> If name ends with "and", such as "Roeland Lastname", citation() will chop 
"and"
  >> as a separate word giving "Roel and Lastname". This is the case in the 
upcoming
  >> release of vegan (1.6-8) just submitted to CRAN. Basically, this seems to 
happen
  >> in utils:::as.personList.default
  >> 
  >> > unlist(as.personList("Roeland Lastname"))
  >> name.first name.middle   name.last  name.first name.middle   name.last
  >> ""  ""  "Roel"  ""  ""  "Lastname"
  >> 
  >> and the culprit line seems to be:
  >> 
  >> x <- unlist(strsplit(x, "[[:space:]]?(,|and)[[:space:]]+"))
  >> 
  >> Fortunately, persons like Anders Andtfolk and Mandalay Grandjean are not
  >> chopped, because they don't have space after "and".

  > I'm sure it'll annoy Anders|George Sand, Bertrand Russell, Inge
  > Helland, et al., but it hardly counts as release-critical, nor trivial
  > enough to slip in during code freeze, especially as regular
  > expressions are involved (does one *ever* get them right on the first
  > try?)

Certainly not release critical ... especially as the conversion
doesn't claim to work in all cases and is there only for convenience:

person("Roeland", "Lastname")

does the right thing, so one can write a correct CITATION file.

unlist(strsplit(x, "[[:space:]]?(,|[[:space:]]and)[[:space:]]+"))


should do the trick, I'll put it into the patched branch after
release.

.f

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[Rd] orphaning CRAN packages

[Friedrich . Leisch]

Dear R Developers,

the following CRAN packages do not cleanly pass R CMD check for quite
some time now and did not have any updates since the time
given. Several attempts by the CRAN admins to contact the package
maintainers had no success.

norm, 1.0-9, 2002-05-07, WARN
sound, 0.6, 2002-08-31, WARN
Bhat, 0.9-07, 2003-11-04, WARN
HI, 0.1, 2003-11-04, WARN
mmlcr, 1.3.2, 2003-11-15, WARN
mvnmle, 0.1-4, 2003-08-21, WARN

If you are the author or maintainer of one of these packages, or a
user and are interested that the package stays in the main CRAN
package area (including binaries for various platforms), please
consider taking over as maintainer of the respective
package. Otheriwse we will orphanize the packages after the release of
R 2.1.0 in 10 days.


In addition, the Orphaned directory of CRAN currently contains

anm,2004-09-30,1.9.1
fdim,2004-09-30,1.9.1
kza,2005-01-15,2.0.1
meanscore,2004-09-30,1.9.1
npmc,2004-09-30,1.9.1
phyloarray,2004-09-30,1.9.1
seao.gui,2004-09-30,1.9.1
seao,2004-09-30,1.9.1
twostage,2004-09-30,1.9.1


We try hard to keep all packages on CRAN working "out of the box",
hence we need to remove packages that are no longer actively
maintained.

Best,
Fritz

-- 
---
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Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch

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Re: [Rd] edit(vignette(...))

[Friedrich . Leisch]

> On Sun, 20 Mar 2005 11:52:11 -0500,
> Paul Gilbert (PG) wrote:

  > I have been looking at edit(vignette(...)) in r-devel, which I think 
  > will be really useful for people working through vignettes. Is there a 
  > way to fork the editor so that the R prompt is returned?
  > The call seems 
  > to be passed though to edit.file, but I don't see any simple way to get 
  > the prompt back until the editor is closed.  (I seem to recall there was 
  > a problem with the prompt returning too soon from bug.report some
  > time ago.)

On windows it does work, if you use the default internal editor. I
played a little bit with file.edit on Unix, but the problem is that
you know much less about the system, a lot of shells and editors could
possibly be involved ... maybe there is a simple solution, but I
failed to see it back then. Probably file.edit() could do with a
"background" argument.


  > I also noticed that many (most?) packages have a vignette with the same 
  > name as the package. Is this considered the standard now?

No, probably most authors are to lazy too invent another name, and of
course it also makes it easier for the user to remember the name of
the vignette ... but we have not written down any standard.

.f

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Re: [Rd] Does cat("\a") ring a bell?

[Friedrich . Leisch]

> On Mon, 7 Mar 2005 21:12:17 +0100,
> stefano iacus (si) wrote:

  > no, on Mac OS X, but could be easily implemented.
  > stefano

  > On 07/mar/05, at 21:02, Duncan Murdoch wrote:

  >> Under GUIs other than Windows (Mac OS X, ESS, etc.) does
  >> 
  >> cat("\a")
  >> 
  >> still make a bell (or some other) sound?  If so, I'll add a "bell()"
  >> function to utils.
  >> 

On Linux:

xterm/gnome-terminal:   yes
ESS no

.f

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Re: [Rd] Wishlist: simple legend options (PR#7400)

[Friedrich . Leisch]

> On Mon, 14 Feb 2005 12:28:20 +0100,
> Gregor GORJANC (GG) wrote:

  > I added link to https://svn.r-project.org/R/trunk/NEWS in files
  > http://www.bfro.uni-lj.si/MR/ggorjan/sources.html
  > http://www.bfro.uni-lj.si/MR/ggorjan/banner.shtml

Thanks, I have copied those to CRAN with only minor modifications.

Best,
Fritz

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Re: [Rd] Documentation bug (PR#7483)

[Friedrich . Leisch]

>>>>> On Sat, 8 Jan 2005 21:37:09 + (GMT),
>>>>> Prof Brian Ripley (PBR) wrote:

  > http://cran.r-project.org is not part of R per se and has its own b=
ug=20
  > reporting address, [EMAIL PROTECTED]

  > That file was made with makeinfo 4.6, and it is a bug in that versi=
on of=20
  > makeinfo.

  > It is not a problem in the version distributed with R for Windows, =
for=20
  > example, made with the current makeinfo 4.7.

Thanks for the bug report, has been fixed.

Best,

--=20
-------
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Institut f=FCr Statistik Tel: (+43 1) 58801 10715
Technische Universit=E4t WienFax: (+43 1) 58801 10798
Wiedner Hauptstra=DFe 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch

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Re: [Rd] Broken Link for gregmisc_2.0.0.zip

[Friedrich . Leisch]

> On Thu, 06 Jan 2005 08:50:44 +0100,
> Uwe Ligges (UL) wrote:

  > Peter Dalgaard wrote:
  >> "Warnes, Gregory R" <[EMAIL PROTECTED]> writes:
  >> 
  >> 
  >>> The link from
  >>> http://cran.r-project.org/src/contrib/Descriptions/gregmisc.html to the
  >>> windows package  gregmisc_2.0.0.zip is broken.  
  >> 
  >> 
  >> Looks like a generic errors in mirroring the windows packages. Has
  >> happened before.

  > Not quite, Windows packages are mirrored correctly, but all (?) links to 
  > Windows *and* Mac OS X binary packages in the packages' Descriptions on 
  > CRAN are broken.

Sorry, my fault. I included the index building in a cron job and that
was broken. Should work now.

  > Uwe

  >> 
  >>> Also, could the appropriate email address for reporting web site problems
  >>> please be added to the website in some conspicous place?
  >> 
  >> 
  >> Good idea.
  >> 

Not really ... we had the webmaster address on almost all pages of
CRAN until 2 or 3 years ago. I removed it deliberately from most
places because way too many people confused it with r-help.

And I doubt that people like Greg really have problems finding out how
to contact Kurt or me ;-)

Best.
Fritz

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Re: [Rd] a better "source(echo=TRUE)" {was "....how to pause...."}

[Friedrich . Leisch]

> On Tue, 30 Nov 2004 12:51:12 +0100,
> Martin Maechler (MM) wrote:

[...]

  > But to do this might be more tricky than at first thought:
  > Of course you can readLines() the source file and writeLines()
  > them to whatever your console is. The slightly difficult thing
  > is to "see" which junks to ``send to R'' , i.e. to parse() and eval().
  > The basic problem seems to see when expressions are complete.

> Maybe we should / could think about enhancing parse() {or a new
  > function with extended behavior} such that it would not only
  > return the parse()d expressions, but also indices (byte or even
  > line counters) to the source text, indicating where each of the
  > expression started and ended.

  > That way I could see a way to proceed.

Yes, that would be also *very* handy for Sweave, where I parse/deparse
exactly for the reasons Martin describes: to get complete expressions
and to know where output should be inserted.

.f

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Re: [Rd] pixmap package and pdf Device.

[Friedrich . Leisch]

>>>>> On Wed, 24 Nov 2004 17:45:58 +0100,
>>>>> Wolski  (W) wrote:

  > Hi,
  > The following code generates a invalid (?) pdf file.

  > pdf("test.pdf")
  > x <- pixmapIndexed(rep(1:8, 9), nrow=6, col=terrain.colors(8))
  > plot(x)
  > dev.off()

  > This pdf can be viewed but not printed 
  > Trying to print causes to crash gv as well as acrobat windows XP

Works fine for me on linux.

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Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch

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Re: [Rd] R-exts.texi: suggestion for small change to Vignette section (PR#7323)

[Friedrich . Leisch]

> On Fri, 29 Oct 2004 12:47:46 +0200 (CEST),
> S J Eglen (SJE) wrote:

  > I recently wrote a vignette, with the following at the top of the .Rnw
  > file:

  > %%\VignetteIndexEntry{How to use look up tables for h() functions}
  > %%\VignetteDepends{sjedmin, spatstat}

  > Using vExplorer() on this function, I got an error from this part of
  > getVigInfo():

  > lines <- grep("^%[[:space:]]*Vignette", file)
  > if (length(lines) == 0) 
  > stop("File ", vig, " does not appear to be a vignette file, ", 
  > "no vignette metadata available.")

  > The error occurs here because the grep expects only one % at the start
  > of the line, whereas I had %%.  (I often use two at the start of a
  > line as I'm used to the ESS/Emacs coding habits of putting ## at the
  > start of a line.)  Changing %% to % solved the problem okay.  

  > So, my minor suggestion to R-exts.texi, at line 1011:

  > @code{\VignetteIndexEntry} statement is best placed in [EMAIL PROTECTED] comment,

  > is that maybe it should say either:

  > "in a [EMAIL PROTECTED] comment"

  > or 

  > "in a [EMAIL PROTECTED] comment with a single %"

  > although admittedly that sounds a bit clunky!


That's a bug in getVigInfo(), not a bug in the R documentation (I also
use %% for the same reason).

Jeff: the regexp should certainly be ^%+[[:space:]]*Vignette", but
there is now also code in package tools which can be used to extract
the info directly.

Best,
Fritz

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Re: [Rd] R-exts.texi: suggestion for small change to Vignette section (PR#7325)

[Friedrich . Leisch]

> On Fri, 29 Oct 2004 12:47:46 +0200 (CEST),
> S J Eglen (SJE) wrote:

  > I recently wrote a vignette, with the following at the top of the .Rnw
  > file:

  > %%\VignetteIndexEntry{How to use look up tables for h() functions}
  > %%\VignetteDepends{sjedmin, spatstat}

  > Using vExplorer() on this function, I got an error from this part of
  > getVigInfo():

  > lines <- grep("^%[[:space:]]*Vignette", file)
  > if (length(lines) == 0) 
  > stop("File ", vig, " does not appear to be a vignette file, ", 
  > "no vignette metadata available.")

  > The error occurs here because the grep expects only one % at the start
  > of the line, whereas I had %%.  (I often use two at the start of a
  > line as I'm used to the ESS/Emacs coding habits of putting ## at the
  > start of a line.)  Changing %% to % solved the problem okay.  

  > So, my minor suggestion to R-exts.texi, at line 1011:

  > @code{\VignetteIndexEntry} statement is best placed in [EMAIL PROTECTED] comment,

  > is that maybe it should say either:

  > "in a [EMAIL PROTECTED] comment"

  > or 

  > "in a [EMAIL PROTECTED] comment with a single %"

  > although admittedly that sounds a bit clunky!


That's a bug in getVigInfo(), not a bug in the R documentation (I also
use %% for the same reason).

Jeff: the regexp should certainly be ^%+[[:space:]]*Vignette", but
there is now also code in package tools which can be used to extract
the info directly.

Best,
Fritz

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RE: [Rd] news file included in source but not binary package

[Friedrich . Leisch]

> On Thu, 24 Jun 2004 10:37:49 -0400,
> Liaw, Andy (LA) wrote:

  > Thanks to Brian, Roger and Dirk for the pointer to inst.  I do remember it,
  > but R-exts doesn't really suggest what that directory is for, merely what
  > would happen to files placed there.  For a source package, though, that
  > seems a rather obscure place to put a `NEWS' file...

I agree ...

  > On a slightly different topic:  May I suggest inclusion of something like
  > the following (suitably modified, if need be) in the next version of R (and
  > perhaps even advertise it in the startup message)?

  > news <- function(package=NULL, lib.loc=NULL) {
  > if (is.null(package)) {
  > file.show(file.path(R.home(), "NEWS"),
  >   title=paste("NEWS for R-",
  >   paste(R.version[c("major", "minor")], collapse=".")))
  > } else {
  > ## check if package is installed
  > pkgs <- installed.packages(lib.loc=lib.loc)
  > which <- match(package, pkgs[, "Package"])
  > if (is.na(which)) stop(package, "not found")
  > newsfile <- file.path(pkgs[which, "LibPath"], "NEWS")
  > if (!file.exists(newsfile)) stop("Sorry, no news from Lake
  > Wobegon...")
  > file.show(newsfile, title=paste("NEWS for ",
  > paste(pkgs[which, c("Package", "Version")],
  >   collapse="_")))
  > }
  > }


You might want to take a look at the system.file() function, that
reduces the above quite condiderably :-)

But to get to the heart of the email (something similar was proposed
by Greg Warnes a few weeks ago): We should definetely provide a simple
mechanism to see the latest changes in a package.

Question: I am aware of files calles NEWS and ChangeLog (or CHANGELOG,
etc.) holding the relevant information ... are there any others we
want/need to respect?

best,
fritz

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Re: [Rd] stdout == 'Terminal' or 'File' {was 'bad interaction ...'}

[Friedrich . Leisch]

> On Wed, 12 May 2004 11:23:56 +0200,
> Martin Maechler (MM) wrote:


  > and maybe we (R developers) should also consider setting some of
  > these (e.g. STERM = "Rgui" in that case) -- at least when the
  > info is available (and somewhat reliable) and even better think
  > about what else (better) could be done, working with  options()
  > settings as a workaround for this problem.

yes

  > Also (for the original topic), maybe  Sweave() could set
  > options(STERM = 'Sweave')

fine with me, but ...

  > if options(STERM = 'BATCH) is not good
  > enough.  Then, code like Martin Schlather's use
  >   switch(getOption("STERM"), 
  >  "BATCH" =  { .},
  >  
  >  )

... for applications like this we might want to keep the list of
possible "terminals" as short as possible (and of course as long as
necessary), so we should come up with a list of possible typoes and
then try to set the option wherever necessary.

.f

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Re: [Rd] R-devel from rsync 04/23

[Friedrich . Leisch]

>>>>> On Sat, 24 Apr 2004 08:27:19 +0100 (BST),
>>>>> Prof Brian Ripley (PBR) wrote:

  > But it also happens in 1.9.0 (always worth checking the current release, 
  > surely?)

  > Try CRAN.packages()[121,]

  > The CRAN PACKAGES file contains

  > Package: haplo.score
  > Version: 1.0.2
  > Date: 2002-09-13
  > Title: Score Tests for Association of Traits with Haplotypes when
  >   Linkage Phase is Ambiguous.
  > Author: Charles M. Rowland, David E. Tines, and Daniel J. Schaid
  >  .  R version translation by Gregory R. Warnes

  > Maintainer: Gregory R. Warnes
  > 

  > and that blank line should not be there.  There are a two others:

[...]

  > So, something has changed at CRAN, near midnight BST.


Sorry, my fault. I changed the index creation script to remove all
email adresses in order to reduce the amount of spam package authors
get, and forgot in one place to take care of the possibility of empty
lines. Should be fixed now.

Best,
Fritz

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Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
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Re: [Rd] XP not mentioned on about.html

[Friedrich . Leisch]

>>>>> On Tue, 30 Mar 2004 19:52:04 -0500 (EST),
>>>>> Gabor Grothendieck (GG) wrote:

  > On 

  >http://www.r-project.org/about.html

  > it says, referring to R,

  >"It also compiles and runs on Windows 9x/NT/2000"

  > XP should be added.

Thanks, is fixed.

Best,

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Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071  [EMAIL PROTECTED]
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Re: [Rd] ISBN number registartion

[Friedrich . Leisch]

> On Fri, 13 Feb 2004 13:07:41 -0800,
> Adrian Custer (AC) wrote:

  > Hello all,
  > I notice that the R package, the manuals and even the FAQ have ISBN
  > numbers. I help write the Gnumeric (GNOME's spreadsheet) manual and
  > wondered how you all managed to get those numbers. Also are these
  > numbers interrelated so that if you gain a document, its number would
  > follow from your existing numbers.

  > Any pointers to information would be appreciated.

ISBN numbers can be purchased from a country-specific agency. The R
Foundation currently owns a series of 100 numbers, i.e. all ISBNs of
form 3-900051-xx-y (y is only a checksum).  We can use those freely
for documents we publish, if the respective document is allowed to get
an ISBN (manuals and software are).

For details see www.isbn.org. Where you get free ISBNs depends on the
country of the *publisher*, in case of the R Foundation that is
Austria.

Please let me know if you need more help.

Best,
Fritz

PS: I really like gnumeric :-)

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Re: [Rd] vol 3/3 web link broken

[Friedrich . Leisch]

> On Thu, 22 Jan 2004 10:09:45 -0500,
> Paul Gilbert (PG) wrote:

  > Something appears to be wrong with the web link to the gzipped 
  > postscript version of Rnews vol 3/3 on .

Yes, there was a permission problem, should be fixed now.

.f

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Re: [Rd] address for bug reports? (PR#5171)

[Friedrich . Leisch]

> On Tue, 18 Nov 2003 17:25:11 +0100 (CET),
> Simon Fear (SF) wrote:

  > bug.report() tells me to email to [EMAIL PROTECTED], whereas
  > the Web site http://www.r-project.org/ points me to 
  > [EMAIL PROTECTED]

  > Which should I believe?


both, the generic [EMAIL PROTECTED] is an alias for the true
[EMAIL PROTECTED]

.f

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Re: [Rd] grep in version 1.8 (PR#4231)

[Friedrich . Leisch]

> On Mon, 22 Sep 2003 10:33:29 -0400,
> Paul Gilbert (PG) wrote:

  > [EMAIL PROTECTED] wrote:
  >>> On Mon, 22 Sep 2003 06:07:00 -0400,
  >>> Duncan Murdoch (DM) wrote:
  >>> 
  >>> 
  >> 
  >> > On Sun, 21 Sep 2003 16:58:10 -0500, you wrote:
  >> >> On Sunday 21 September 2003 16:50, Duncan Murdoch wrote:
  >> >>> On Sun, 21 Sep 2003 11:23:57 +0200 (MET DST), you wrote:
  >> >>> >This is not a bug! It works when compiling from clean sources.
  >> >>> >
  >> >>> >I guess you have unpacked new sources over old sources? Please clean the
  >> >>> >directory before unpacking a new version, and try to compile again. A
  >> >>> >couple of us ran in the same problem during the last weeks.
  >> >>> 
  >> >>> I don't know if this is what happened here, but this kind of thing
  >> >>> also happens when using rsync, not just when unpacking tarballs:
  >> >>> rsync won't delete obsolete files.  Anonymous cvs wouldn't have this
  >> >>> problem.
  >> >> 
  >> >> rsync should delete files if you give the --delete flag
  >> 
  >> > Yes, but then you end up doing a clean build, because it will also
  >> > delete the *.o files, etc.  I don't think there's a concept of
  >> > deleting files that were there yesterday but aren't there today.
  >> 
  >> Yes, there is:
  >> 
  >> 1) Use the --delete flag when updating the sources
  >> 
  > (From another strand of this thread)  I don't think the -P option to the 
  > cvs update command does this, it just prunes empty subdirectories, and 
  > -d does roughly the opposite. If cvs has a way to delete files that are 
  > not in the archive I have never found it, and would be curious to know 
  > what it is so that I can be careful to avoid it.

  >> 2) Use a build directory that is different from your source tree, that
  >> way rsync will never see the *.o et al files.
  >> 
  > This is probably the answer, but I don't understand how it solves what I 
  > think was the original question. Could someone please expand on
 
  >   i/  How make will know to ignore certain .o files which should not be 
  > there, but leave other ones that are up-to-date and not rebuild
  > them.

It doesn't work all the time, sometimes a fresh build from scratch is
required. But it works most of the time (I do it every day).

  >   ii/  How to build R in a different  directory from the sources.

On Unix: Simply create and go go to an empty directory and type

PATH/TO/THE/R/SOURCE/TREE/configure

and then proceed as usual, i.e., type

make

etc.

On windows (as I just learned from Duncan) this does not work. I don't
know about the Mac.

.f

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Re: [Rd] grep in version 1.8 (PR#4231)

[Friedrich . Leisch]

>>>>> On Mon, 22 Sep 2003 06:07:00 -0400,
>>>>> Duncan Murdoch (DM) wrote:

  > On Sun, 21 Sep 2003 16:58:10 -0500, you wrote:
  >> On Sunday 21 September 2003 16:50, Duncan Murdoch wrote:
  >>> On Sun, 21 Sep 2003 11:23:57 +0200 (MET DST), you wrote:
  >>> >This is not a bug! It works when compiling from clean sources.
  >>> >
  >>> >I guess you have unpacked new sources over old sources? Please clean the
  >>> >directory before unpacking a new version, and try to compile again. A
  >>> >couple of us ran in the same problem during the last weeks.
  >>> 
  >>> I don't know if this is what happened here, but this kind of thing
  >>> also happens when using rsync, not just when unpacking tarballs:
  >>> rsync won't delete obsolete files.  Anonymous cvs wouldn't have this
  >>> problem.
  >> 
  >> rsync should delete files if you give the --delete flag

  > Yes, but then you end up doing a clean build, because it will also
  > delete the *.o files, etc.  I don't think there's a concept of
  > deleting files that were there yesterday but aren't there today.

Yes, there is:

1) Use the --delete flag when updating the sources
2) Use a build directory that is different from your source tree, that
   way rsync will never see the *.o et al files.

-- 
---
Friedrich Leisch 
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071  [EMAIL PROTECTED]
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch

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Re: [Rd] Sweave: option family=...

[Friedrich . Leisch]

>>>>> On Thu, 18 Sep 2003 11:19:38 +0200,
>>>>> Wolfram Fischer (WF) wrote:

  > I would propose to add an option ``family''
  > to RweaveLatex() resp. RweaveLatexSetup() 
  > in order to be able to set the font family
  > for postscript and pdf graphics:

  > <>=
  > ...
  > @

Why is setting it via ps.options() not sufficient for you?

Best,

-- 
-------
Friedrich Leisch 
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071  [EMAIL PROTECTED]
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch

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Re: [Rd] potentially nasty interaction between R 1.8.0 and tetex

[Friedrich . Leisch]

> On Thu, 11 Sep 2003 09:21:09 -0700,
> A J Rossini (AJR) wrote:


  > Fritz, where is "Blue" and "Red" defined in your distribution?

Hard to say ... seems like graphics/dvipsnam.def contains a couple of
name definitions, all starting with uppercase
letters. graphics/color.sty contains lowercase definitions for the
primary colors, though. So maybe we should simply try

Red -> red
Blue -> blue

and see whether that survives the upcoming testing cycle?

.f

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Re: [Rd] potentially nasty interaction between R 1.8.0 and tetex

[Friedrich . Leisch]

> On 11 Sep 2003 10:30:39 +0200,
> Peter Dalgaard BSA (PDB) wrote:

  > [EMAIL PROTECTED] writes:
  >> > On Wed, 10 Sep 2003 16:21:03 -0700,
  >> > A J Rossini (AJR) wrote:
  >> 
  >> > Peter Dalgaard BSA <[EMAIL PROTECTED]> writes:
  >> >> Change being Blue --> blue, Red --> red in hyperref.cfg I presume? Odd
  >> >> thing is that it doesn't happen with RedHat 8.0 tetex and ordinary
  >> >> "make pdf". Shouldn't the hyperlinks in the manuals have the same
  >> >> problem?
  >> 
  >> > I'm not sure what is called in the case you mention.
  >> 
  >> > Note that this doesn't happen if one uses texi2dvi from the command
  >> > line, either, which is how I traced it down when comparing output in
  >> > the tex log files.
  >> 
  >> > (i.e. the inclusion of the RHOME/share/texmf/hyperref.cfg from "R CMD
  >> > build" and not present when using RHOME/bin/texi2dvi).
  >> 
  >> Hmm, we have this definition of hyperref.cfg since 1.5.0, i.e., quite
  >> some time now. I'm not sure if we really should change anything if
  >> problems are only on Debian unstable machines. I have Debian testing
  >> and that works fine.

  > We'd probably want to take a closer look at what the issue really
  > is,

yes, definitely

  > including teTeX version numbers. It could be a permanent change in
  > teTeX v2+ in which case we're going to see the effect all over the
  > place as it gets into major Linux distros, or it could be an
  > installation problem with Debian-unstable which should go away. 

  > Then again, does "blue" and "Blue" really do different things?

probably not

  > In a
  > "no-op or fix" situation, we might choose to do the change...

I don't know ... the problem is that it is the first time we see this,
and I'd like to avoid that "blue" works for us, we put it in and then
it doesn't work on a lot of other systems. 

My system has:

galadriel:Leisch$ dpkg -l tetex*
ii  tetex-base 2.0.2-4.1  basic teTeX library files
ii  tetex-bin  2.0.2-4.2  teTeX binary files
ii  tetex-doc  2.0.2-4.1  teTeX documentation
ii  tetex-extra2.0.2-4.1  extra teTeX library files



.f

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Re: [Rd] potentially nasty interaction between R 1.8.0 and tetex

[Friedrich . Leisch]

> On Wed, 10 Sep 2003 16:21:03 -0700,
> A J Rossini (AJR) wrote:

  > Peter Dalgaard BSA <[EMAIL PROTECTED]> writes:
  >> Change being Blue --> blue, Red --> red in hyperref.cfg I presume? Odd
  >> thing is that it doesn't happen with RedHat 8.0 tetex and ordinary
  >> "make pdf". Shouldn't the hyperlinks in the manuals have the same
  >> problem?

  > I'm not sure what is called in the case you mention.

  > Note that this doesn't happen if one uses texi2dvi from the command
  > line, either, which is how I traced it down when comparing output in
  > the tex log files.

  > (i.e. the inclusion of the RHOME/share/texmf/hyperref.cfg from "R CMD
  > build" and not present when using RHOME/bin/texi2dvi).

Hmm, we have this definition of hyperref.cfg since 1.5.0, i.e., quite
some time now. I'm not sure if we really should change anything if
problems are only on Debian unstable machines. I have Debian testing
and that works fine.

.f

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Re: [Rd] sweave problem

[Friedrich . Leisch]

> On Wed, 10 Sep 2003 01:05:23 -0400 (EDT),
> Rafael A Irizarry (RAI) wrote:

  > hi!
  > using:
  > Version 1.8.0 Under development (unstable) (2003-09-02)

  > using the Sweave function of the tools package i get this error when
  > latexing with texi2dvi --pdf

  > ! LaTeX Error: File `upquote.sty' not found.

  > if i change the line
  > \usepackage{/users/faculty/ririzarr/R-1.8.0/lib/R/share/texmf/Sweave}
  > to
  > \usepackage{/users/faculty/ririzarr/R-1.7.1/lib/R/share/texmf/Sweave}

  > in the tex file, then the file compiles fine.


  > this happens to me in both redhat 7.3 and solaris 8.


Should be OK if you use a newer version, this was fixed on 2003-09-03,
i.e., a week ago.

best,
fritz

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Re: [Rd] Could not create DVI version

[Friedrich . Leisch]

> On Tue, 1 Apr 2003 19:54:10 +0100 (BST),
> Prof Brian Ripley (PBR) wrote:

[...]

  > I've seen that several times: I think there is an Sweave-related gc 
  > problem.

Anything reproducible?

Paul nd I tried to nail down the problem several times ... but as the
bug didn't shon on our machines, it was impossible for me to track
down the bug yet.

As Sweave uses only S code, it can only be an R bug triggered by
Sweave ...

.f

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Re: [Rd] docs, examples, man pages (PR#2711)

[Friedrich . Leisch]

> On 31 Mar 2003 17:22:29 +0200,
> Peter Dalgaard BSA (PDB) wrote:

  > [EMAIL PROTECTED] writes:
  >> It would be great if the man page had examples for each of the commands.
  >> 
  >> I've got R installed, but
  >> 
  >> info R
  >> 
  >> brings up the page for the GNU regular expression library. Any chance of 
  >> having a complete set of man pages?
  >> 
  >> Plain text documentation is good. I don't use Latex, and no one I know 
  >> uses it.
  >> 
  >> Thanks for a great package!
  >> 
  >> Tom

  > There *is* plaintext help for each command. Two thousand one hundred
  > and ten files of it as of last count, albeit not in info format, but
  > as text, html, and latex. For the same reason, the refman is not an
  > info document but available in .dvi and .pdf formats. However, we
  > might consider building one of the other documents in the manual
  > collection (which are written in texinfo) in info format and put it
  > into the info tree for info-afficionados.

Umm, we do exactly that, the make targets are

make info
make install-info

E.g., typing "info R-intro" in a shell does the expected on my box ...

Best,
Fritz

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[Rd] Re: [R] calling sweave function from latex

[Friedrich . Leisch]

[ Moved to r-devel ]


>>>>> On Wed, 29 Jan 2003 12:17:29 -0500,
>>>>> Frank E Harrell (FEH) wrote:


  > Before I discovered Sweave, I used methods that are detailed in Chapter 13 of 
http://hesweb1.med.virginia.edu/biostat/s/doc/splus.pdf for managing large analysis 
projects.  The do function in the Hmisc library (not yet tested for R) was created to 
manage code chunks that each create their own series of output listings and postscript 
graphics files.  For conditional execution of chunks, it helps me to set flags at the 
start of the document so that I don't have to hunt for any flags or if statements.  I 
do things like

  > importdata<- FALSE
  > fitmodel  <- FALSE
  > validatemodel <- TRUE

  > if(importdata) {
  >  ...
  > }
  > if(fitmodel) {
  >  ...
  > }
  > if(validatemodel) {
  >  ... time-consuming bootstrap code ...
  > }

  > or use

  > do(importdata, { ... code chunk ...})
  > do(fitmodel, {... code chunk ...})
  > do(validatemodel, {... code chunk ...})

  > where the keys such as 'importdata' are used as root names of files created by 
that code chunk.  The 'validatemodel' chunk creates by default 'validatemodel.lst' to 
contain the printed output, and files such as 'validatemodel.ps' for graphics.

  > It would be nice if Sweave could implement this type of model.  In LaTeX I find it 
invaluable to set flags for conditional text insertion using \def and \ifnum \fi.  For 
a report, the text might always be included but S chunks only condionally run, with 
previous output used when a chunk is bypassed.

  > Please take a look at Chapter 13 of the above referenced document if you have 
time, to see if it gives you any ideas worth pursuing.

Thanks a lot, I'll add it to my pile of weekend reading material.

The code you give above looks similar to what I have in mind. Each
chunk can list previous chunks that it depends on (by default all
previous chunks). Sweave will only re-run the chunk if (the parsed
version of) the code has changed, and otherwise re-use the existing
material. Additionally I want to have a hook that allows turning off
evaluation based on chunk names.

I already have an S4 representation of parsed Sweave files, currently
I am working on a representation of the evaluated object (and
functions to get it).

Best,
Fritz

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