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

cstrato cstrato at aon.at
Wed May 4 22:02:05 CEST 2011 

Dear Simon,

I did not complain about the R doing something wrong. I only wanted to 
know why, after all these years, R CMD check does suddenly no longer 
build the pdf-files of the vignettes. I also think that this is a legal 
question.

Let me compare the times spent:

1, the "official" development cycle:
- R CMD build:   5 minutes
- R CMD INSTALL: 3 minutes
- R CMD check:   6 minutes

2, my own development cycle:
- manual tarring: 2 seconds
- R CMD check:    6 minutes

This means spending 14 minutes vs 6 minutes. If I assume that in one 
evening I have to make 10 corrections this would mean 140 minutes vs 60 
minutes, i.e. the official development cycle would take 1 hr and 20 min 
longer than my own development cycle. This is time I do not have.

Best regards
Christian


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

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