From ripley at stats.ox.ac.uk  Mon May  2 07:08:26 2011
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Mon, 2 May 2011 06:08:26 +0100 (BST)
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
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Message-ID: <alpine.LFD.2.02.1105020549360.441@gannet.stats.ox.ac.uk>

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
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595


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