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

Mon May 9 20:40:50 CEST 2011

Dear Herve,

Since 'R CMD check' has already options '--no-vignettes' and 
'--no-rebuild-vignettes', so why not option '--no-clean-vignettes'?
But, as you admitted, it is only a suggestion.

Maybe it is time to close this thread.
(If you want we can discuss this issue further privately.)

Best regards
Christian

On 5/9/11 7:20 AM, Hervé Pagès wrote:
> Christian,
>
> On 11-05-08 01:19 PM, cstrato wrote:
>> 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
>
> and then someone tried to explain you that you didn't need that,
> you just need to use the standard development cycle. And in your
> last 5 emails you're still trying to convince the people around
> that you have a better/faster development cycle that doesn't use
> 'R CMD build' at all. No matter this better development cycle is
> broken, it should be supported anyway by adding a
> "--no-clean-vignettes" option to 'R CMD check' just because
> that would be a "convenient option for you"? I know, you are
> just suggesting this option, but still...
>
> H.
>
>>
>> Best regards
>> Christian
>>
>>
>> On 5/8/11 9:29 PM, Hervé Pagès 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
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