From cstrato at aon.at  Tue May  3 23:15:56 2011
From: cstrato at aon.at (cstrato)
Date: Tue, 03 May 2011 23:15:56 +0200
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
In-Reply-To: <602EC185-8BED-4EF4-B2AF-2EDF29B6EE84@r-project.org>
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>
	<602EC185-8BED-4EF4-B2AF-2EDF29B6EE84@r-project.org>
Message-ID: <4DC0708C.2060708@aon.at>

No, I simply do "tar czf xps_1.13.1.tar.gz xps".

Best regards
Christian


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?
cstrato