From cstrato at aon.at  Sun May  8 22:19:51 2011
From: cstrato at aon.at (cstrato)
Date: Sun, 08 May 2011 22:19:51 +0200
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
In-Reply-To: <4DC6EF10.3040308@fhcrc.org>
References: <4DB32D9F.5010406@aon.at>	<4DB42FB3.9090401@statistik.tu-dortmund.de>	<4DB472F8.9060903@aon.at>	<4DB489EC.9080301@statistik.tu-dortmund.de>	<4DB491BE.8080104@aon.at>	<4DB57E7A.1080507@statistik.tu-dortmund.de>	<4DB5AFD4.9020303@aon.at>
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Message-ID: <4DC6FAE7.6090106@aon.at>

Dear Herve,

In my initial mail:
https://stat.ethz.ch/pipermail/r-devel/2011-April/060688.html
I wrote: "While R CMD check and R CMD INSTALL have always created the 
vignettes on R-2.12.1 or any earlier versions of R, I am no longer able 
to build the vignettes on R-2.13.0."

Although I made the mistake to include R CMD INSTALL, I wanted simply to 
know why R CMD check suddenly (after all these years) does no longer 
build the pdf-versions of the vignettes.

After many replies and discussions Prof. Ripley gave finally the answer:
https://stat.ethz.ch/pipermail/r-devel/2011-May/060782.html

I understand the reason for this and made the suggestion to include an 
option such as "--no-clean-vignettes" to R CMD check, since this would 
be a convenient option for me:
https://stat.ethz.ch/pipermail/r-devel/2011-May/060797.html

Best regards
Christian


On 5/8/11 9:29 PM, Herv? Pag?s wrote:
> Hi Christian,
>
> On 11-05-04 01:02 PM, cstrato wrote:
>> Dear Simon,
>>
>> I did not complain about the R doing something wrong. I only wanted to
>> know why, after all these years, R CMD check does suddenly no longer
>> build the pdf-files of the vignettes. I also think that this is a legal
>> question.
>>
>> Let me compare the times spent:
>>
>> 1, the "official" development cycle:
>> - R CMD build: 5 minutes
>> - R CMD INSTALL: 3 minutes
>> - R CMD check: 6 minutes
>>
>> 2, my own development cycle:
>> - manual tarring: 2 seconds
>> - R CMD check: 6 minutes
>>
>> This means spending 14 minutes vs 6 minutes.
>
> My understanding is that R CMD INSTALL is not strictly necessary in
> the official devel cycle. However, to be fair you should either include
> that step in both cycles (devel and yours) or not. Then the numbers are
> 14 minutes vs 9 minutes (or 11 minutes vs 6 minutes).
>
>> If I assume that in one
>> evening I have to make 10 corrections this would mean 140 minutes vs 60
>> minutes, i.e. the official development cycle would take 1 hr and 20 min
>> longer than my own development cycle. This is time I do not have.
>
> No matter how you put it and how much benefits you get from this,
> manual tarring is *wrong* and "after all these years" you should really
> know this. Furthermore, here is what you claimed in a previous email:
>
> This is my development cycle:
>
> First, I run R CMD check until there are no more warnings/errors.
> Since years it was very convenient that R CMD check builds the
> pdf-files of the vignettes, too, since this allowed me to correct
> errors in the manual files and the vignette files at the same time!
>
> Afterwards I run R CMD INSTALL to install my package and do more
> tests until everything works.
>
> As you see I do not use R CMD build, since every run takes about
> 5 minutes, it overwrites my zipped source code, and I would need
> to unzip it to get access to the vignette pdf-files.
>
> You didn't mention the manual tarring.
>
> Then later:
>
> Thank you, however since I use "R CMD INSTALL xps.tar.gz" my source
> code is not polluted.
>
> So you are contradicting yourself.
>
> No, I simply do "tar czf xps_1.13.1.tar.gz xps".
>
> Whaooo, finally! Note that, among other problems, this manual tarring
> is very likely to pollute your source tree (this is one of the things
> R CMD build will take care of).
>
> You are free to do manual tarring for your own internal business if
> you want, nobody cares, but you should keep this kind of dirty little
> secrets for you. For your 10 corrections, you can do manual tarring
> 10 times, that's your problem, but that doesn't prevent you from doing
> the right thing, i.e. R CMD build + R CMD check, as a *final* pass (e.g.
> just before you commit your changes to svn). Now that means 71 minutes
> vs 60 minutes, but you did the *right* thing.
>
> Cheers,
> H.
>
>
>
>>
>> Best regards
>> Christian
>>
>>
>> On 5/4/11 12:13 AM, Simon Urbanek wrote:
>>> On May 3, 2011, at 5:15 PM, cstrato wrote:
>>>
>>>> No, I simply do "tar czf xps_1.13.1.tar.gz xps".
>>>>
>>>
>>> Well, that's your problem then, not R's. Source packages are created
>>> using R CMD build, not by manual tarring (you can do the latter if you
>>> know what you're doing, but then you can't complain about the R doing
>>> something wrong).
>>>
>>> Cheers,
>>> S
>>>
>>>
>>>>
>>>> On 5/3/11 11:11 PM, Simon Urbanek wrote:
>>>>> On May 3, 2011, at 4:48 PM, cstrato<cstrato at aon.at> wrote:
>>>>>
>>>>>> Dear Uwe,
>>>>>>
>>>>>> Thank you, however since I use "R CMD INSTALL xps.tar.gz" my source
>>>>>> code is not polluted.
>>>>>>
>>>>>
>>>>> But then you already used build to create the tar ball so the
>>>>> vignette has been built. So what is your point?
>>>>>
>>>>> Cheers,
>>>>> S
>>>>>
>>>>>
>>>>>> Furthermore, I forgot to mention that finally I upload the source
>>>>>> code only to the BioC svn repository. The rest is done by the BioC
>>>>>> servers, including building the pdf-files for the vignettes.
>>>>>>
>>>>>> Best regards
>>>>>> Christian
>>>>>>
>>>>>>
>>>>>> On 5/3/11 10:13 PM, Uwe Ligges wrote:
>>>>>>>
>>>>>>>
>>>>>>> On 03.05.2011 21:14, cstrato wrote:
>>>>>>>> Dear Uwe,
>>>>>>>>
>>>>>>>> This is my development cycle:
>>>>>>>>
>>>>>>>> First, I run R CMD check until there are no more warnings/errors.
>>>>>>>> Since
>>>>>>>> years it was very convenient that R CMD check builds the
>>>>>>>> pdf-files of
>>>>>>>> the vignettes, too, since this allowed me to correct errors in the
>>>>>>>> manual files and the vignette files at the same time!
>>>>>>>>
>>>>>>>> Afterwards I run R CMD INSTALL to install my package and do more
>>>>>>>> tests
>>>>>>>> until everything works.
>>>>>>>>
>>>>>>>> As you see I do not use R CMD build, since every run takes about 5
>>>>>>>> minutes, it overwrites my zipped source code, and I would need to
>>>>>>>> unzip
>>>>>>>> it to get access to the vignette pdf-files.
>>>>>>>
>>>>>>>
>>>>>>> Then this is the main problem here. The *recommended* development
>>>>>>> cycle
>>>>>>> from the manuals is to run
>>>>>>>
>>>>>>> 1. R CMD build in order to get a valid source tarball and clean
>>>>>>> the sources
>>>>>>> 2. R CMD INSTALL to check if your package can be installed
>>>>>>> 3. R CMD check in order to finally check your package
>>>>>>>
>>>>>>> Running R CMD INSTALL on your source directory may pollute it, hence
>>>>>>> this is not recommended at all.
>>>>>>>
>>>>>>>
>>>>>>> Best,
>>>>>>> UWe
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>> Best regards
>>>>>>>> Christian
>>>>>>>>
>>>>>>>>
>>>>>>>> On 5/3/11 1:07 PM, Uwe Ligges wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 02.05.2011 21:24, cstrato wrote:
>>>>>>>>>> Dear Prof. Ripley,
>>>>>>>>>>
>>>>>>>>>> Thank you for your confirmation and explanation, I understand the
>>>>>>>>>> reason
>>>>>>>>>> for cleaning things up to save memory. However, it was very
>>>>>>>>>> convenient
>>>>>>>>>> to have this feature in earlier versions of R. It would be really
>>>>>>>>>> helpful to have an additional option to R CMD check, e.g.
>>>>>>>>>> "--no-clean-vignettes".
>>>>>>>>>>
>>>>>>>>>> FYI, I did not claim "..create the vignettes *in<pkg>inst/doc*",
>>>>>>>>>> instead my words were:
>>>>>>>>>> One interesting observation is that xps.Rcheck from R-2.12.2
>>>>>>>>>> contains
>>>>>>>>>> the subdirectory "inst/doc" with the vignettes while xps.Rcheck
>>>>>>>>>> from
>>>>>>>>>> R-2.13.0 does not contain "inst".
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> But you do not need it. I do not know how often I have to
>>>>>>>>> mention that
>>>>>>>>> vignettes are produced by R CMD build! They are already build when
>>>>>>>>> running R CMD check. And please do not tell us about tzhe PDF
>>>>>>>>> version
>>>>>>>>> oif manuals which are *unrelated* to vignettes, because they are
>>>>>>>>> not
>>>>>>>>> built in advance and need to be checked, since they should be
>>>>>>>>> produced
>>>>>>>>> at user level while vignettes are built at developer level
>>>>>>>>> already.
>>>>>>>>>
>>>>>>>>> Uwe Ligges
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Best regards
>>>>>>>>>> Christian
>>>>>>>>>> _._._._._._._._._._._._._._._._._._
>>>>>>>>>> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
>>>>>>>>>> V.i.e.n.n.a A.u.s.t.r.i.a
>>>>>>>>>> e.m.a.i.l: cstrato at aon.at
>>>>>>>>>> _._._._._._._._._._._._._._._._._._
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 5/2/11 7:08 AM, Prof Brian Ripley wrote:
>>>>>>>>>>> On Sun, 1 May 2011, Duncan Murdoch wrote:
>>>>>>>>>>>
>>>>>>>>>>>> On 11-05-01 4:10 PM, cstrato wrote:
>>>>>>>>>>>>> Dear Duncan, dear Uwe,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Since I have installed both WinXP and OpenSUSE 11.3 on my
>>>>>>>>>>>>> Mac in a
>>>>>>>>>>>>> virtual machine, I have now done the following tests on all
>>>>>>>>>>>>> three
>>>>>>>>>>>>> architectures:
>>>>>>>>>>>>>
>>>>>>>>>>>>> 1, R CMD build xps:
>>>>>>>>>>>>> This creates "xps_1.13.1.tar.gz" which DOES contain all
>>>>>>>>>>>>> vignettes as
>>>>>>>>>>>>> pdf-file. Thus R CMD build is ok.
>>>>>>>>>>>>>
>>>>>>>>>>>>> 2, R CMD check xps:
>>>>>>>>>>>>> This does NOT build the vignettes as pdf-files on all three
>>>>>>>>>>>>> architectures. Or to be more precise, R-2.13.0 does no
>>>>>>>>>>>>> longer build
>>>>>>>>>>>>> the
>>>>>>>>>>>>> vignettes since with R-2.12.2 and earlier versions R did
>>>>>>>>>>>>> create the
>>>>>>>>>>>>> vignettes as pdf-files.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thus the question is:
>>>>>>>>>>>>> Why does R CMD check no longer create the vignettes?
>>>>>>>>>>>>
>>>>>>>>>>>> Probably the answer is simply "because it doesn't". For a truly
>>>>>>>>>>>> reliable check, you should build the package, then check the
>>>>>>>>>>>> tar.gz
>>>>>>>>>>>> file. Anything else is, and always has been, an approximation.
>>>>>>>>>>>
>>>>>>>>>>> Actually, it does. What earlier versions never did (despite
>>>>>>>>>>> 'cstrato's
>>>>>>>>>>> repeated delusional claims earlier) was to create the
>>>>>>>>>>> vignettes *in
>>>>>>>>>>> <pkg>inst/doc*. All of them re-created (by default) vignettes
>>>>>>>>>>> in a
>>>>>>>>>>> working directory. The difference is that 2.13.0 deletes that
>>>>>>>>>>> working
>>>>>>>>>>> directory if the test was successful, whereas earlier versions
>>>>>>>>>>> left
>>>>>>>>>>> the
>>>>>>>>>>> results somewhere in<pkg>.Rcheck (the 'somewhere' has varied).
>>>>>>>>>>> However,
>>>>>>>>>>> earier versions of R CMD check sometimes failed when R CMD build
>>>>>>>>>>> succeeded
>>>>>>>>>>>
>>>>>>>>>>> Using Animal (a small CRAN package with one vignette).
>>>>>>>>>>>
>>>>>>>>>>> R 2.12.2 gave
>>>>>>>>>>>
>>>>>>>>>>> * checking package vignettes in ?inst/doc? ... WARNING
>>>>>>>>>>> Package vignettes without corresponding PDF:
>>>>>>>>>>> /tmp/Animal/inst/doc/Animal.Rnw
>>>>>>>>>>>
>>>>>>>>>>> and the vignette was re-created in Animal.Rcheck/inst/doc.
>>>>>>>>>>>
>>>>>>>>>>> R 2.13.0 gives
>>>>>>>>>>>
>>>>>>>>>>> * checking package vignettes in ?inst/doc? ... WARNING
>>>>>>>>>>> Package vignette(s) without corresponding PDF:
>>>>>>>>>>> Animal.Rnw
>>>>>>>>>>>
>>>>>>>>>>> Non-ASCII package vignette(s) without specified encoding:
>>>>>>>>>>> Animal.Rnw
>>>>>>>>>>>
>>>>>>>>>>> * checking running R code from vignettes ... OK
>>>>>>>>>>> * checking re-building of vignettes ... OK
>>>>>>>>>>>
>>>>>>>>>>> and the working directory was Animal.Rcheck/vign_test .
>>>>>>>>>>>
>>>>>>>>>>> The main reason for cleaning up is that to mimic R CMD build
>>>>>>>>>>> the test
>>>>>>>>>>> has to make a complete copy of the package sources, and that
>>>>>>>>>>> adds up:
>>>>>>>>>>> checking CRAN already takes 17GB for each flavour.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Duncan Murdoch
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Best regards
>>>>>>>>>>>>> Christian
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On 4/27/11 10:16 AM, Uwe Ligges wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On 26.04.2011 21:58, cstrato wrote:
>>>>>>>>>>>>>>> Dear Duncan, dear Uwe,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Just now I have re-run everything, and today xps.Rnw can be
>>>>>>>>>>>>>>> converted to
>>>>>>>>>>>>>>> a vignette w/o any problems using:
>>>>>>>>>>>>>>> a, buildVignettes("xps", dir="/Volumes/CoreData/CRAN/xps",
>>>>>>>>>>>>>>> quiet=F)
>>>>>>>>>>>>>>> b, R CMD Sweave xps.Rnw
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> In both cases the vignette xps.pdf is created (maybe my
>>>>>>>>>>>>>>> Mac did
>>>>>>>>>>>>>>> not
>>>>>>>>>>>>>>> like
>>>>>>>>>>>>>>> to work during eastern holidays).
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> However, one issue remains:
>>>>>>>>>>>>>>> "R64 CMD check xps_1.13.1.tar.gz" no longer creates any
>>>>>>>>>>>>>>> pdf files
>>>>>>>>>>>>>>> for
>>>>>>>>>>>>>>> the vignettes.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Dioes it give an error or warning? It should check the
>>>>>>>>>>>>>> code. R CMD
>>>>>>>>>>>>>> build
>>>>>>>>>>>>>> creates the pdf files.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Uwe Ligges
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Best regards
>>>>>>>>>>>>>>> Christian
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On 4/25/11 9:31 PM, Duncan Murdoch wrote:
>>>>>>>>>>>>>>>> On 25/04/2011 3:16 PM, cstrato wrote:
>>>>>>>>>>>>>>>>> Thank you.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> My problem seems to be that at the moment the problem
>>>>>>>>>>>>>>>>> can be
>>>>>>>>>>>>>>>>> seen
>>>>>>>>>>>>>>>>> only
>>>>>>>>>>>>>>>>> on my Mac, since e.g. the Bioconductor servers have no
>>>>>>>>>>>>>>>>> problems
>>>>>>>>>>>>>>>>> creating
>>>>>>>>>>>>>>>>> the vignettes.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Then you are definitely the one in the best position to
>>>>>>>>>>>>>>>> diagnose
>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>> problem. Use the usual approach: simplify it by cutting out
>>>>>>>>>>>>>>>> everything
>>>>>>>>>>>>>>>> that looks unrelated. Verify that the problem still
>>>>>>>>>>>>>>>> exists, then
>>>>>>>>>>>>>>>> cut
>>>>>>>>>>>>>>>> some more. Eventually you'll have isolated the error to a
>>>>>>>>>>>>>>>> particular
>>>>>>>>>>>>>>>> small snippet of code, and then you can add print()
>>>>>>>>>>>>>>>> statements, or
>>>>>>>>>>>>>>>> use
>>>>>>>>>>>>>>>> trace(), or do whatever is necessary to see what's so
>>>>>>>>>>>>>>>> special
>>>>>>>>>>>>>>>> about your
>>>>>>>>>>>>>>>> system.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I suspect it will turn out to be an assumption in the code
>>>>>>>>>>>>>>>> that is
>>>>>>>>>>>>>>>> not
>>>>>>>>>>>>>>>> true on your system.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> If the assumption is being made by code you wrote, then fix
>>>>>>>>>>>>>>>> it. If
>>>>>>>>>>>>>>>> it's
>>>>>>>>>>>>>>>> being made by R, let us know.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Duncan Murdoch
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Best regards
>>>>>>>>>>>>>>>>> Christian
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On 4/25/11 8:55 PM, Duncan Murdoch wrote:
>>>>>>>>>>>>>>>>>> cstrato wrote:
>>>>>>>>>>>>>>>>>>> Dear Duncan,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thank you for your example, however it is different
>>>>>>>>>>>>>>>>>>> since it
>>>>>>>>>>>>>>>>>>> does not
>>>>>>>>>>>>>>>>>>> use x and y. What about print(x+y)?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Try it.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Sorry, I do not believe that there is a bug in my
>>>>>>>>>>>>>>>>>>> code, since:
>>>>>>>>>>>>>>>>>>> 1, it worked in all versions from R starting with
>>>>>>>>>>>>>>>>>>> R-2.6.0 till
>>>>>>>>>>>>>>>>>>> R-2.12.2.
>>>>>>>>>>>>>>>>>>> 2, the identical code works in the examples
>>>>>>>>>>>>>>>>>>> 3, this code (or a similar code) is the starting code
>>>>>>>>>>>>>>>>>>> which
>>>>>>>>>>>>>>>>>>> all
>>>>>>>>>>>>>>>>>>> users
>>>>>>>>>>>>>>>>>>> of xps have to use, and there was never a problem.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> This might be a problem in R, or might be a problem in
>>>>>>>>>>>>>>>>>> your
>>>>>>>>>>>>>>>>>> code. As
>>>>>>>>>>>>>>>>>> far
>>>>>>>>>>>>>>>>>> as I know, it has only shown up in your code, so I'd
>>>>>>>>>>>>>>>>>> guess
>>>>>>>>>>>>>>>>>> that's
>>>>>>>>>>>>>>>>>> where
>>>>>>>>>>>>>>>>>> the problem is. In any case, you're the one in the best
>>>>>>>>>>>>>>>>>> position to
>>>>>>>>>>>>>>>>>> isolate it and debug it.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> If it turns out to be a problem in R, put together an
>>>>>>>>>>>>>>>>>> example
>>>>>>>>>>>>>>>>>> illustrating the problem that doesn't involve your
>>>>>>>>>>>>>>>>>> code, and
>>>>>>>>>>>>>>>>>> I'll
>>>>>>>>>>>>>>>>>> take a
>>>>>>>>>>>>>>>>>> look.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Duncan Murdoch
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Maybe the reason could be that my code has to import
>>>>>>>>>>>>>>>>>>> - the CEL-files from the package dir
>>>>>>>>>>>>>>>>>>> - the file SchemeTest3.root from the package dir
>>>>>>>>>>>>>>>>>>> ??
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Best regards
>>>>>>>>>>>>>>>>>>> Christian
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On 4/25/11 8:00 PM, Duncan Murdoch wrote:
>>>>>>>>>>>>>>>>>>>> cstrato wrote:
>>>>>>>>>>>>>>>>>>>>> Dear Uwe,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Your suggestion to look at the Sweave manual helped
>>>>>>>>>>>>>>>>>>>>> me to
>>>>>>>>>>>>>>>>>>>>> solve the
>>>>>>>>>>>>>>>>>>>>> problem. It seems that in R-2.13.0 every chunk can
>>>>>>>>>>>>>>>>>>>>> use the
>>>>>>>>>>>>>>>>>>>>> code
>>>>>>>>>>>>>>>>>>>>> from
>>>>>>>>>>>>>>>>>>>>> the chunk before but not from an earlier chunk.
>>>>>>>>>>>>>>>>>>>> I'm either misreading what you wrote, or it's wrong.
>>>>>>>>>>>>>>>>>>>> If I
>>>>>>>>>>>>>>>>>>>> have
>>>>>>>>>>>>>>>>>>>> this
>>>>>>>>>>>>>>>>>>>> in a
>>>>>>>>>>>>>>>>>>>> Sweave file:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> <<>>=
>>>>>>>>>>>>>>>>>>>> x<- 1
>>>>>>>>>>>>>>>>>>>> @
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> <<>>=
>>>>>>>>>>>>>>>>>>>> y<- 2
>>>>>>>>>>>>>>>>>>>> @
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> <<>>=
>>>>>>>>>>>>>>>>>>>> print(x)
>>>>>>>>>>>>>>>>>>>> @
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I will see the value of x getting printed, even
>>>>>>>>>>>>>>>>>>>> though it
>>>>>>>>>>>>>>>>>>>> came
>>>>>>>>>>>>>>>>>>>> from
>>>>>>>>>>>>>>>>>>>> two
>>>>>>>>>>>>>>>>>>>> chunks earlier.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I think Uwe is right: there is some bug in the code
>>>>>>>>>>>>>>>>>>>> you're
>>>>>>>>>>>>>>>>>>>> running.
>>>>>>>>>>>>>>>>>>>> Sweave isn't the problem.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Duncan Murdoch
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Concretely, the following does not work since chunk
>>>>>>>>>>>>>>>>>>>>> 5 needs
>>>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>>>> code
>>>>>>>>>>>>>>>>>>>>> from chunk 3 and 4:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>> ### chunk number 3:
>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>> #line 126 "xps.Rnw"
>>>>>>>>>>>>>>>>>>>>> celdir<- file.path(.path.package("xps"), "raw")
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>> ### chunk number 4:
>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>> #line 132 "xps.Rnw"
>>>>>>>>>>>>>>>>>>>>> scheme.test3<-
>>>>>>>>>>>>>>>>>>>>> root.scheme(file.path(.path.package("xps"),
>>>>>>>>>>>>>>>>>>>>> "schemes",
>>>>>>>>>>>>>>>>>>>>> "SchemeTest3.root"))
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>> ### chunk number 5:
>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>> #line 137 "xps.Rnw"
>>>>>>>>>>>>>>>>>>>>> celfiles<- c("TestA1.CEL","TestA2.CEL")
>>>>>>>>>>>>>>>>>>>>> data.test3<- import.data(scheme.test3,
>>>>>>>>>>>>>>>>>>>>> "tmpdt_DataTest3",
>>>>>>>>>>>>>>>>>>>>> celdir=celdir, celfiles=celfiles, verbose=FALSE)
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> However, when I add "celdir" to chunk 5 then
>>>>>>>>>>>>>>>>>>>>> everything
>>>>>>>>>>>>>>>>>>>>> works
>>>>>>>>>>>>>>>>>>>>> since
>>>>>>>>>>>>>>>>>>>>> now chunk 5 needs only the code from chunk 4 but not
>>>>>>>>>>>>>>>>>>>>> from
>>>>>>>>>>>>>>>>>>>>> chunk 3:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>> ### chunk number 5:
>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>> #line 137 "xps.Rnw"
>>>>>>>>>>>>>>>>>>>>> celdir<- file.path(.path.package("xps"), "raw")
>>>>>>>>>>>>>>>>>>>>> celfiles<- c("TestA1.CEL","TestA2.CEL")
>>>>>>>>>>>>>>>>>>>>> data.test3<- import.data(scheme.test3,
>>>>>>>>>>>>>>>>>>>>> "tmpdt_DataTest3",
>>>>>>>>>>>>>>>>>>>>> celdir=celdir, celfiles=celfiles, verbose=FALSE)
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Now buildVignettes() is able to create the vignettes,
>>>>>>>>>>>>>>>>>>>>> however
>>>>>>>>>>>>>>>>>>>>> R CMD
>>>>>>>>>>>>>>>>>>>>> check still does not build the vignettes.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Yes, I get a Warning in both cases:
>>>>>>>>>>>>>>>>>>>>> * checking package vignettes in 'inst/doc' ... WARNING
>>>>>>>>>>>>>>>>>>>>> Package vignettes without corresponding PDF: ........
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> However, with R-2.12.2 the following lines are added:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> /Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/APTvsXPS.Rnw
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> /Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/xps.Rnw
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> /Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/xpsClasses.Rnw
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> /Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/xpsPreprocess.Rnw
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> and in xps.Rcheck the subdirectory "inst/doc" will be
>>>>>>>>>>>>>>>>>>>>> created
>>>>>>>>>>>>>>>>>>>>> which
>>>>>>>>>>>>>>>>>>>>> contains the vignette data such as xps.Rnw, but also
>>>>>>>>>>>>>>>>>>>>> xps.tex
>>>>>>>>>>>>>>>>>>>>> and
>>>>>>>>>>>>>>>>>>>>> xps.pdf.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> In contrast, R-2.13.0 does not create the subdirectory
>>>>>>>>>>>>>>>>>>>>> "inst/doc"
>>>>>>>>>>>>>>>>>>>>> and
>>>>>>>>>>>>>>>>>>>>> no vignettes are built.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> One more issue:
>>>>>>>>>>>>>>>>>>>>> In contrast to my former believe R CMD INSTALL does
>>>>>>>>>>>>>>>>>>>>> not
>>>>>>>>>>>>>>>>>>>>> build
>>>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>>>> vignettes, neither in R-2.12.2 nor in R-2.13.0. I
>>>>>>>>>>>>>>>>>>>>> have to
>>>>>>>>>>>>>>>>>>>>> run
>>>>>>>>>>>>>>>>>>>>> buildVignettes() after installation. Is this the
>>>>>>>>>>>>>>>>>>>>> usual case?
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Best regards
>>>>>>>>>>>>>>>>>>>>> Christian
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On 4/25/11 4:00 PM, Uwe Ligges wrote:
>>>>>>>>>>>>>>>>>>>>>> On 24.04.2011 23:10, cstrato wrote:
>>>>>>>>>>>>>>>>>>>>>>> Dear Uwe,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> On 4/24/11 10:37 PM, Uwe Ligges wrote:
>>>>>>>>>>>>>>>>>>>>>>>> On 24.04.2011 20:59, cstrato wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> Dear Uwe,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for your reply.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ad 2, Yes, i know that "xps-manual.pdf" is the
>>>>>>>>>>>>>>>>>>>>>>>>> collection of
>>>>>>>>>>>>>>>>>>>>>>>>> help
>>>>>>>>>>>>>>>>>>>>>>>>> pages,
>>>>>>>>>>>>>>>>>>>>>>>>> I have mentioned it only to show that creating
>>>>>>>>>>>>>>>>>>>>>>>>> pdf-files
>>>>>>>>>>>>>>>>>>>>>>>>> does
>>>>>>>>>>>>>>>>>>>>>>>>> work
>>>>>>>>>>>>>>>>>>>>>>>>> for
>>>>>>>>>>>>>>>>>>>>>>>>> R-2.13.0.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ad 1, Could it be that this is a Mac-specific
>>>>>>>>>>>>>>>>>>>>>>>>> problem
>>>>>>>>>>>>>>>>>>>>>>>>> since I
>>>>>>>>>>>>>>>>>>>>>>>>> see
>>>>>>>>>>>>>>>>>>>>>>>>> it on
>>>>>>>>>>>>>>>>>>>>>>>>> both my old MacBook Pro and my new Mac Mini.
>>>>>>>>>>>>>>>>>>>>>>>> Have you tried on any other OS? I did not since
>>>>>>>>>>>>>>>>>>>>>>>> installing
>>>>>>>>>>>>>>>>>>>>>>>> root is
>>>>>>>>>>>>>>>>>>>>>>>> a bit
>>>>>>>>>>>>>>>>>>>>>>>> too much effort.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> No, until now I did not try another OS, but I
>>>>>>>>>>>>>>>>>>>>>>> will, since
>>>>>>>>>>>>>>>>>>>>>>> xps
>>>>>>>>>>>>>>>>>>>>>>> has to
>>>>>>>>>>>>>>>>>>>>>>> work on all three OSes.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Using R CMD check with R-2.12.2 I get:
>>>>>>>>>>>>>>>>>>>>>>>> I thought we are talking about R-2.13.0?
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> I showed you the output of R-2.12.2 first and then
>>>>>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>>>>>> output of
>>>>>>>>>>>>>>>>>>>>>>> R-2.13.0, so that you can see that on the same
>>>>>>>>>>>>>>>>>>>>>>> machine
>>>>>>>>>>>>>>>>>>>>>>> with
>>>>>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>>>>>> same
>>>>>>>>>>>>>>>>>>>>>>> file it works with one version but not the other.
>>>>>>>>>>>>>>>>>>>>>> But you got a Warning in both cases:
>>>>>>>>>>>>>>>>>>>>>> * checking package vignettes in 'inst/doc' ...
>>>>>>>>>>>>>>>>>>>>>> WARNING
>>>>>>>>>>>>>>>>>>>>>> Package vignettes without corresponding PDF: ........
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Where is the R CMD build output (since R CMD
>>>>>>>>>>>>>>>>>>>>>>>> build is
>>>>>>>>>>>>>>>>>>>>>>>> supposed to
>>>>>>>>>>>>>>>>>>>>>>>> prepare the vignette).
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> $ R64 CMD check xps_1.13.1.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>> * using log directory
>>>>>>>>>>>>>>>>>>>>>>>>> '/Volumes/CoreData/CRAN/xps.Rcheck'
>>>>>>>>>>>>>>>>>>>>>>>>> * using R version 2.12.2 (2011-02-25)
>>>>>>>>>>>>>>>>>>>>>>>>> * using platform: x86_64-apple-darwin9.8.0
>>>>>>>>>>>>>>>>>>>>>>>>> (64-bit)
>>>>>>>>>>>>>>>>>>>>>>>>> * using session charset: ASCII
>>>>>>>>>>>>>>>>>>>>>>>>> * checking for file 'xps/DESCRIPTION' ... OK
>>>>>>>>>>>>>>>>>>>>>>>>> * this is package 'xps' version '1.13.1'
>>>>>>>>>>>>>>>>>>>>>>>>> ...
>>>>>>>>>>>>>>>>>>>>>>>>> ...
>>>>>>>>>>>>>>>>>>>>>>>>> * checking package vignettes in 'inst/doc' ...
>>>>>>>>>>>>>>>>>>>>>>>>> WARNING
>>>>>>>>>>>>>>>>>>>>>>>>> Package vignettes without corresponding PDF:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> /Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/APTvsXPS.Rnw
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> /Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/xps.Rnw
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> /Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/xpsClasses.Rnw
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> /Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/xpsPreprocess.Rnw
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> * checking PDF version of manual ... OK
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Using "RSwitch.app" I switch to R-2.13.0, but
>>>>>>>>>>>>>>>>>>>>>>>>> now I get:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> $ R64 CMD check xps_1.13.1.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>> * using log directory
>>>>>>>>>>>>>>>>>>>>>>>>> '/Volumes/CoreData/CRAN/xps.Rcheck'
>>>>>>>>>>>>>>>>>>>>>>>>> * using R version 2.13.0 (2011-04-13)
>>>>>>>>>>>>>>>>>>>>>>>>> * using platform: x86_64-apple-darwin9.8.0
>>>>>>>>>>>>>>>>>>>>>>>>> (64-bit)
>>>>>>>>>>>>>>>>>>>>>>>>> * using session charset: ASCII
>>>>>>>>>>>>>>>>>>>>>>>>> * checking for file 'xps/DESCRIPTION' ... OK
>>>>>>>>>>>>>>>>>>>>>>>>> * this is package 'xps' version '1.13.1'
>>>>>>>>>>>>>>>>>>>>>>>>> ...
>>>>>>>>>>>>>>>>>>>>>>>>> ...
>>>>>>>>>>>>>>>>>>>>>>>>> * checking package vignettes in 'inst/doc' ...
>>>>>>>>>>>>>>>>>>>>>>>>> WARNING
>>>>>>>>>>>>>>>>>>>>>>>>> Package vignette(s) without corresponding PDF:
>>>>>>>>>>>>>>>>>>>>>>>>> APTvsXPS.Rnw
>>>>>>>>>>>>>>>>>>>>>>>>> xps.Rnw
>>>>>>>>>>>>>>>>>>>>>>>>> xpsClasses.Rnw
>>>>>>>>>>>>>>>>>>>>>>>>> xpsPreprocess.Rnw
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> * checking running R code from vignettes ... OK
>>>>>>>>>>>>>>>>>>>>>>>>> * checking re-building of vignettes ... OK
>>>>>>>>>>>>>>>>>>>>>>>>> * checking PDF version of manual ... OK
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> I must admit that I have never built the vignettes
>>>>>>>>>>>>>>>>>>>>>>>>> manually,
>>>>>>>>>>>>>>>>>>>>>>>>> and I
>>>>>>>>>>>>>>>>>>>>>>>>> cannot find a hint how I can do it from the
>>>>>>>>>>>>>>>>>>>>>>>>> command
>>>>>>>>>>>>>>>>>>>>>>>>> line. Is
>>>>>>>>>>>>>>>>>>>>>>>>> this
>>>>>>>>>>>>>>>>>>>>>>>>> possible?
>>>>>>>>>>>>>>>>>>>>>>> Is it possible to build the vignettes from the
>>>>>>>>>>>>>>>>>>>>>>> command
>>>>>>>>>>>>>>>>>>>>>>> line?
>>>>>>>>>>>>>>>>>>>>>> R --help suggests there is
>>>>>>>>>>>>>>>>>>>>>> R CMD Sweave .....
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> However, building the vignettes within R-2.13.0
>>>>>>>>>>>>>>>>>>>>>>>>> I get:
>>>>>>>>>>>>>>>>>>>>>>>>>> library(tools)
>>>>>>>>>>>>>>>>>>>>>>>>>> buildVignettes("xps",
>>>>>>>>>>>>>>>>>>>>>>>>>> dir="/Volumes/CoreData/CRAN/xps",
>>>>>>>>>>>>>>>>>>>>>>>>>> quiet=F)
>>>>>>>>>>>>>>>>>>>>>>>>> Overfull ?vbox (21.68121pt too high) has
>>>>>>>>>>>>>>>>>>>>>>>>> occurred while
>>>>>>>>>>>>>>>>>>>>>>>>> ?output is
>>>>>>>>>>>>>>>>>>>>>>>>> Writing to file xps.tex
>>>>>>>>>>>>>>>>>>>>>>>>> Processing code chunks with options ...
>>>>>>>>>>>>>>>>>>>>>>>>> 1 : term verbatim
>>>>>>>>>>>>>>>>>>>>>>>>> 2 : echo term hide
>>>>>>>>>>>>>>>>>>>>>>>>> 3 : echo term verbatim
>>>>>>>>>>>>>>>>>>>>>>>>> 4 : echo term verbatim
>>>>>>>>>>>>>>>>>>>>>>>>> 5 : echo term verbatim
>>>>>>>>>>>>>>>>>>>>>>>>> SysError in<TFile::TFile>: file
>>>>>>>>>>>>>>>>>>>>>>>>> /tmpdt_DataTest3_cel.root/tmpdt_DataTest3_cel_20110424_201301.root
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> can
>>>>>>>>>>>>>>>>>>>>>>>>> not be opened (No such file or directory)
>>>>>>>>>>>>>>>>>>>>>>>>> Error: Could not create
>>>>>>>>>>>>>>>>>>>>>>>>> file</tmpdt_DataTest3_cel.root>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Here are the two important chunks 4 and 5, which
>>>>>>>>>>>>>>>>>>>>>>>>> work
>>>>>>>>>>>>>>>>>>>>>>>>> fine with
>>>>>>>>>>>>>>>>>>>>>>>>> R-2.12.2
>>>>>>>>>>>>>>>>>>>>>>>>> and earlier versions:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ### chunk number 4:
>>>>>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> #line 132 "xps.Rnw"
>>>>>>>>>>>>>>>>>>>>>>>>> scheme.test3<-
>>>>>>>>>>>>>>>>>>>>>>>>> root.scheme(file.path(.path.package("xps"),
>>>>>>>>>>>>>>>>>>>>>>>>> "schemes",
>>>>>>>>>>>>>>>>>>>>>>>>> "SchemeTest3.root"))
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ### chunk number 5:
>>>>>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> #line 137 "xps.Rnw"
>>>>>>>>>>>>>>>>>>>>>>>>> celfiles<- c("TestA1.CEL","TestA2.CEL")
>>>>>>>>>>>>>>>>>>>>>>>>> data.test3<- import.data(scheme.test3,
>>>>>>>>>>>>>>>>>>>>>>>>> "tmpdt_DataTest3",
>>>>>>>>>>>>>>>>>>>>>>>>> celdir=celdir, celfiles=celfiles, verbose=FALSE)
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> However, in R-2.13.0 chunk 5 crashes!!!
>>>>>>>>>>>>>>>>>>>>>>>>> It works only when replacing chunk 5 with:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ### chunk number 5:
>>>>>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> #line 137 "xps.Rnw"
>>>>>>>>>>>>>>>>>>>>>>>>> celfiles<- c("TestA1.CEL","TestA2.CEL")
>>>>>>>>>>>>>>>>>>>>>>>>> scheme.test3<-
>>>>>>>>>>>>>>>>>>>>>>>>> root.scheme(file.path(.path.package("xps"),
>>>>>>>>>>>>>>>>>>>>>>>>> "schemes",
>>>>>>>>>>>>>>>>>>>>>>>>> "SchemeTest3.root"))
>>>>>>>>>>>>>>>>>>>>>>>>> data.test3<- import.data(scheme.test3,
>>>>>>>>>>>>>>>>>>>>>>>>> "tmpdt_DataTest3",
>>>>>>>>>>>>>>>>>>>>>>>>> celdir=celdir, celfiles=celfiles, verbose=FALSE)
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> As you see R-2.13.0 does no longer remember the
>>>>>>>>>>>>>>>>>>>>>>>>> result of
>>>>>>>>>>>>>>>>>>>>>>>>> chunk 4,
>>>>>>>>>>>>>>>>>>>>>>>>> i.e.
>>>>>>>>>>>>>>>>>>>>>>>>> "scheme.test3". Now I have to include the line
>>>>>>>>>>>>>>>>>>>>>>>>> defining
>>>>>>>>>>>>>>>>>>>>>>>>> "scheme.test3"
>>>>>>>>>>>>>>>>>>>>>>>>> also in chunk 5.
>>>>>>>>>>>>>>>>>>>>>>>> How objects generated in one chunk can be reused
>>>>>>>>>>>>>>>>>>>>>>>> later
>>>>>>>>>>>>>>>>>>>>>>>> on is
>>>>>>>>>>>>>>>>>>>>>>>> explained
>>>>>>>>>>>>>>>>>>>>>>>> in the Sweave manual.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Do you have any idea for this behavior?
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> An example, which does work in R-2.13.0 are the
>>>>>>>>>>>>>>>>>>>>>>>>> following
>>>>>>>>>>>>>>>>>>>>>>>>> two
>>>>>>>>>>>>>>>>>>>>>>>>> chunks:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> #################################################
>>>>>>>>>>>>>>>>>>>>>>>>> ### chunk number 20:
>>>>>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> #line 300 "xps.Rnw"
>>>>>>>>>>>>>>>>>>>>>>>>> library(xps)
>>>>>>>>>>>>>>>>>>>>>>>>> scheme.test3<-
>>>>>>>>>>>>>>>>>>>>>>>>> root.scheme(file.path(.path.package("xps"),
>>>>>>>>>>>>>>>>>>>>>>>>> "schemes",
>>>>>>>>>>>>>>>>>>>>>>>>> "SchemeTest3.root"))
>>>>>>>>>>>>>>>>>>>>>>>>> data.test3<- root.data(scheme.test3,
>>>>>>>>>>>>>>>>>>>>>>>>> file.path(.path.package("xps"),"rootdata",
>>>>>>>>>>>>>>>>>>>>>>>>> "DataTest3_cel.root"))
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ### chunk number 21:
>>>>>>>>>>>>>>>>>>>>>>>>> ###################################################
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> #line 318 "xps.Rnw"
>>>>>>>>>>>>>>>>>>>>>>>>> data.rma<- rma(data.test3, "tmpdt_Test3RMA",
>>>>>>>>>>>>>>>>>>>>>>>>> verbose=FALSE)
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> In summary it is not quite clear to me what has
>>>>>>>>>>>>>>>>>>>>>>>>> changed in
>>>>>>>>>>>>>>>>>>>>>>>>> R-2.13.0 so
>>>>>>>>>>>>>>>>>>>>>>>>> that chunk 5 no longer works.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> BTW, the error:
>>>>>>>>>>>>>>>>>>>>>>>>> SysError in<TFile::TFile>: file
>>>>>>>>>>>>>>>>>>>>>>>>> /tmpdt_DataTest3_cel.root/tmpdt_DataTest3_cel_20110424_201301.root
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> can
>>>>>>>>>>>>>>>>>>>>>>>>> not be opened
>>>>>>>>>>>>>>>>>>>>>>>>> is not clear to me since
>>>>>>>>>>>>>>>>>>>>>>>>> "/tmpdt_DataTest3_cel.root/" is
>>>>>>>>>>>>>>>>>>>>>>>>> definitively
>>>>>>>>>>>>>>>>>>>>>>>>> NOT a directory.
>>>>>>>>>>>>>>>>>>>>>>>> Time to debug what root.scheme is doing with the
>>>>>>>>>>>>>>>>>>>>>>>> supplied
>>>>>>>>>>>>>>>>>>>>>>>> path.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Sorry, I do not understand what you mean.
>>>>>>>>>>>>>>>>>>>>>>> root.scheme does
>>>>>>>>>>>>>>>>>>>>>>> not
>>>>>>>>>>>>>>>>>>>>>>> change
>>>>>>>>>>>>>>>>>>>>>>> the path, otherwise it would not work on all older
>>>>>>>>>>>>>>>>>>>>>>> versions
>>>>>>>>>>>>>>>>>>>>>>> of R.
>>>>>>>>>>>>>>>>>>>>>> Right, but since something changed obviously, and
>>>>>>>>>>>>>>>>>>>>>> you tell
>>>>>>>>>>>>>>>>>>>>>> us the
>>>>>>>>>>>>>>>>>>>>>> path
>>>>>>>>>>>>>>>>>>>>>> is not a path, it might be a function used by
>>>>>>>>>>>>>>>>>>>>>> root.scheme
>>>>>>>>>>>>>>>>>>>>>> ....
>>>>>>>>>>>>>>>>>>>>>> That's
>>>>>>>>>>>>>>>>>>>>>> why I said time to debug the code in your vignette!
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Do you have any ideas?
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Please note that the vignette "xps.Rnw" did work
>>>>>>>>>>>>>>>>>>>>>>>>> for the
>>>>>>>>>>>>>>>>>>>>>>>>> last
>>>>>>>>>>>>>>>>>>>>>>>>> two
>>>>>>>>>>>>>>>>>>>>>>>>> years
>>>>>>>>>>>>>>>>>>>>>>>>> w/o problem. Furthermore, the Bioconductor
>>>>>>>>>>>>>>>>>>>>>>>>> servers are
>>>>>>>>>>>>>>>>>>>>>>>>> able to
>>>>>>>>>>>>>>>>>>>>>>>>> build
>>>>>>>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>>>>>>>> vignette, see:
>>>>>>>>>>>>>>>>>>>>>>>>> http://www.bioconductor.org/packages/release/bioc/html/xps.html
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> See
>>>>>>>>>>>>>>>>>>>>>>>> http://bioconductor.org/checkResults/2.8/bioc-20110225/xps/liverpool-checksrc.html
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> and find that their Mac Servers are also fine
>>>>>>>>>>>>>>>>>>>>>>>> with it. So
>>>>>>>>>>>>>>>>>>>>>>>> maybe
>>>>>>>>>>>>>>>>>>>>>>>> it is
>>>>>>>>>>>>>>>>>>>>>>>> your setup that is corrupted?
>>>>>>>>>>>>>>>>>>>>>>> Maybe, you are right that my setup is corrupted,
>>>>>>>>>>>>>>>>>>>>>>> but on
>>>>>>>>>>>>>>>>>>>>>>> two
>>>>>>>>>>>>>>>>>>>>>>> independent
>>>>>>>>>>>>>>>>>>>>>>> machines?
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Maybe the download of "R-2.13.0.pkg" is corrupted,
>>>>>>>>>>>>>>>>>>>>>>> but
>>>>>>>>>>>>>>>>>>>>>>> then
>>>>>>>>>>>>>>>>>>>>>>> nothing
>>>>>>>>>>>>>>>>>>>>>>> should work, or am I wrong?
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> How can I check if my setup is corrupted?
>>>>>>>>>>>>>>>>>>>>>> By debugging the code in your package's vignette.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Uwe Ligges
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Best regards
>>>>>>>>>>>>>>>>>>>>>>> Christian
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Best wishes,
>>>>>>>>>>>>>>>>>>>>>>>> Uwe
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Best regards
>>>>>>>>>>>>>>>>>>>>>>>>> Christian
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> On 4/24/11 4:12 PM, Uwe Ligges wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> On 23.04.2011 21:50, cstrato wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear all,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> While R CMD check and R CMD INSTALL have always
>>>>>>>>>>>>>>>>>>>>>>>>>>> created
>>>>>>>>>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>>>>>>>>>> vignettes on
>>>>>>>>>>>>>>>>>>>>>>>>>>> R-2.12.1 or any earlier versions of R, I am no
>>>>>>>>>>>>>>>>>>>>>>>>>>> longer
>>>>>>>>>>>>>>>>>>>>>>>>>>> able to
>>>>>>>>>>>>>>>>>>>>>>>>>>> build
>>>>>>>>>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>>>>>>>>>> vignettes on R-2.13.0.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Instead R CMD check gives me the following
>>>>>>>>>>>>>>>>>>>>>>>>>>> output:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> * checking for unstated dependencies in
>>>>>>>>>>>>>>>>>>>>>>>>>>> vignettes
>>>>>>>>>>>>>>>>>>>>>>>>>>> ... OK
>>>>>>>>>>>>>>>>>>>>>>>>>>> * checking package vignettes in 'inst/doc' ...
>>>>>>>>>>>>>>>>>>>>>>>>>>> WARNING
>>>>>>>>>>>>>>>>>>>>>>>>>>> Package vignette(s) without corresponding PDF:
>>>>>>>>>>>>>>>>>>>>>>>>>>> APTvsXPS.Rnw
>>>>>>>>>>>>>>>>>>>>>>>>>>> xps.Rnw
>>>>>>>>>>>>>>>>>>>>>>>>>>> xpsClasses.Rnw
>>>>>>>>>>>>>>>>>>>>>>>>>>> xpsPreprocess.Rnw
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> * checking running R code from vignettes ... OK
>>>>>>>>>>>>>>>>>>>>>>>>>>> * checking re-building of vignettes ... OK
>>>>>>>>>>>>>>>>>>>>>>>>>>> * checking PDF version of manual ... OK
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Does someone know what the reason might be?
>>>>>>>>>>>>>>>>>>>>>>>>>> No, it does for me for other packages.
>>>>>>>>>>>>>>>>>>>>>>>>>> Perhaps an error when processing the vignettes?
>>>>>>>>>>>>>>>>>>>>>>>>>> Have
>>>>>>>>>>>>>>>>>>>>>>>>>> you
>>>>>>>>>>>>>>>>>>>>>>>>>> tried to
>>>>>>>>>>>>>>>>>>>>>>>>>> build
>>>>>>>>>>>>>>>>>>>>>>>>>> them manually?
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> (R64 CMD check --help says that be default
>>>>>>>>>>>>>>>>>>>>>>>>>>> rebuild-vignettes is
>>>>>>>>>>>>>>>>>>>>>>>>>>> turned
>>>>>>>>>>>>>>>>>>>>>>>>>>> on.)
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Interestingly, R CMD check still creates the
>>>>>>>>>>>>>>>>>>>>>>>>>>> file
>>>>>>>>>>>>>>>>>>>>>>>>>>> "xps-manual.pdf".
>>>>>>>>>>>>>>>>>>>>>>>>>> That is the collection of help pages, unrelated
>>>>>>>>>>>>>>>>>>>>>>>>>> to the
>>>>>>>>>>>>>>>>>>>>>>>>>> vignette.
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Uwe Ligges
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Here is my sessionInfo:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> sessionInfo()
>>>>>>>>>>>>>>>>>>>>>>>>>>> R version 2.13.0 (2011-04-13)
>>>>>>>>>>>>>>>>>>>>>>>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64
>>>>>>>>>>>>>>>>>>>>>>>>>>> (64-bit)
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> locale:
>>>>>>>>>>>>>>>>>>>>>>>>>>> [1] C
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> attached base packages:
>>>>>>>>>>>>>>>>>>>>>>>>>>> [1] stats graphics grDevices utils datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>> methods
>>>>>>>>>>>>>>>>>>>>>>>>>>> base
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> other attached packages:
>>>>>>>>>>>>>>>>>>>>>>>>>>> [1] xps_1.13.1
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> loaded via a namespace (and not attached):
>>>>>>>>>>>>>>>>>>>>>>>>>>> [1] Biobase_2.12.1 Biostrings_2.20.0
>>>>>>>>>>>>>>>>>>>>>>>>>>> IRanges_1.10.0
>>>>>>>>>>>>>>>>>>>>>>>>>>> [4] affy_1.30.0 affyPLM_1.28.5 affyio_1.20.0
>>>>>>>>>>>>>>>>>>>>>>>>>>> [7] preprocessCore_1.14.0
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you in advance.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Best regards
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christian
>>>>>>>>>>>>>>>>>>>>>>>>>>> _._._._._._._._._._._._._._._._._._
>>>>>>>>>>>>>>>>>>>>>>>>>>> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
>>>>>>>>>>>>>>>>>>>>>>>>>>> V.i.e.n.n.a A.u.s.t.r.i.a
>>>>>>>>>>>>>>>>>>>>>>>>>>> e.m.a.i.l: cstrato at aon.at
>>>>>>>>>>>>>>>>>>>>>>>>>>> _._._._._._._._._._._._._._._._._._
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> ______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>> R-devel at r-project.org mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>>>>>>>>>>>>>>>>>>>>> ______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> R-devel at r-project.org mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>>>>>>>>>>>>>>>>> ______________________________________________
>>>>>>>>>>>>>>>>>>>>> R-devel at r-project.org mailing list
>>>>>>>>>>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ______________________________________________
>>>>>>>>>>>> R-devel at r-project.org mailing list
>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ______________________________________________
>>>>>>>>>> R-devel at r-project.org mailing list
>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>>>>>
>>>>>>>
>>>>>>
>>>>>> ______________________________________________
>>>>>> R-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>
>>>>
>>>>
>>>
>>>
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>



[Rd] How to create vignette.pdf for R-2.13.0?
cstrato