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

Duncan Murdoch murdoch.duncan at gmail.com
Mon May 2 01:19:43 CEST 2011 

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.

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
>>>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>

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