From simon.urbanek at r-project.org  Tue May  3 23:11:12 2011
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Tue, 3 May 2011 17:11:12 -0400
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
In-Reply-To: <4DC06A03.2010205@aon.at>
References: <4DB32D9F.5010406@aon.at>
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	<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>
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	<4DC06A03.2010205@aon.at>
Message-ID: <602EC185-8BED-4EF4-B2AF-2EDF29B6EE84@r-project.org>

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



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