From hpages at fhcrc.org  Mon May  9 07:20:04 2011
From: hpages at fhcrc.org (=?windows-1252?Q?Herv=E9_Pag=E8s?=)
Date: Sun, 08 May 2011 22:20:04 -0700
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
In-Reply-To: <4DC6FAE7.6090106@aon.at>
References: <4DB32D9F.5010406@aon.at>	<4DB42FB3.9090401@statistik.tu-dortmund.de>	<4DB472F8.9060903@aon.at>	<4DB489EC.9080301@statistik.tu-dortmund.de>	<4DB491BE.8080104@aon.at>	<4DB57E7A.1080507@statistik.tu-dortmund.de>	<4DB5AFD4.9020303@aon.at>
	<4DB5B6B0.90607@gmail.com>	<4DB5C286.40306@aon.at>
	<4DB5C38D.6030400@gmail.com>	<4DB5C87C.5040905@aon.at>
	<4DB5CBFD.6050508@gmail.com>	<4DB723F9.7090800@aon.at>	<4DB7D0DD.6040201@statistik.tu-dortmund.de>	<4DBDBE4F.8020702@aon.at>
	<4DBDEA8F.60000@gmail.com>	<alpine.LFD.2.02.1105020549360.441@gannet.stats.ox.ac.uk>	<4DBF04E4.8020806@aon.at>	<4DBFE206.3030708@statistik.tu-dortmund.de>	<4DC05427.7060908@aon.at>	<4DC061D1.3080105@statistik.tu-dortmund.de>	<4DC06A03.2010205@aon.at>	<602EC185-8BED-4EF4-B2AF-2EDF29B6EE84@r-project.org>	<4DC0708C.2060708@aon.at>	<CB833A13-DB66-45F1-B45C-D79AAC819B17@r-project.org>
	<4DC1B0BD.6030509@aon.at> <4DC6EF10.3040308@fhcrc.org>
	<4DC6FAE7.6090106@aon.at>
Message-ID: <4DC77984.6020005@fhcrc.org>

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


-- 
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?
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