From cstrato at aon.at  Tue May  3 22:48:03 2011
From: cstrato at aon.at (cstrato)
Date: Tue, 03 May 2011 22:48:03 +0200
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
In-Reply-To: <4DC061D1.3080105@statistik.tu-dortmund.de>
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>
Message-ID: <4DC06A03.2010205@aon.at>

Dear Uwe,

Thank you, however since I use "R CMD INSTALL xps.tar.gz" my source code 
is not polluted.

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
>>>
>



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