From ligges at statistik.tu-dortmund.de  Tue May  3 22:13:05 2011
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Tue, 03 May 2011 22:13:05 +0200
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
In-Reply-To: <4DC05427.7060908@aon.at>
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Message-ID: <4DC061D1.3080105@statistik.tu-dortmund.de>



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
>>



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