From ligges at statistik.tu-dortmund.de  Wed Apr 27 10:16:29 2011
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Wed, 27 Apr 2011 10:16:29 +0200
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
In-Reply-To: <4DB723F9.7090800@aon.at>
References: <4DB32D9F.5010406@aon.at>	<4DB42FB3.9090401@statistik.tu-dortmund.de>	<4DB472F8.9060903@aon.at>	<4DB489EC.9080301@statistik.tu-dortmund.de>	<4DB491BE.8080104@aon.at>	<4DB57E7A.1080507@statistik.tu-dortmund.de>
	<4DB5AFD4.9020303@aon.at> <4DB5B6B0.90607@gmail.com>
	<4DB5C286.40306@aon.at> <4DB5C38D.6030400@gmail.com>
	<4DB5C87C.5040905@aon.at> <4DB5CBFD.6050508@gmail.com>
	<4DB723F9.7090800@aon.at>
Message-ID: <4DB7D0DD.6040201@statistik.tu-dortmund.de>



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



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