From hpages at fhcrc.org  Sun May  8 21:29:20 2011
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Date: Sun, 08 May 2011 12:29:20 -0700
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
In-Reply-To: <4DC1B0BD.6030509@aon.at>
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	<4DC1B0BD.6030509@aon.at>
Message-ID: <4DC6EF10.3040308@fhcrc.org>

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


-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



[Rd] How to create vignette.pdf for R-2.13.0?
=?windows-1252?Q?Herv=E9_Pag=E8s?=