From simon.urbanek at r-project.org  Wed May  4 00:13:27 2011
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Tue, 3 May 2011 18:13:27 -0400
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
In-Reply-To: <4DC0708C.2060708@aon.at>
References: <4DB32D9F.5010406@aon.at>
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	<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>
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	<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>
Message-ID: <CB833A13-DB66-45F1-B45C-D79AAC819B17@r-project.org>

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
>> 
> 
> 



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