From ligges at statistik.tu-dortmund.de  Tue May  3 13:07:50 2011
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Tue, 03 May 2011 13:07:50 +0200
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
In-Reply-To: <4DBF04E4.8020806@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>	<4DB7D0DD.6040201@statistik.tu-dortmund.de>	<4DBDBE4F.8020702@aon.at>
	<4DBDEA8F.60000@gmail.com>	<alpine.LFD.2.02.1105020549360.441@gannet.stats.ox.ac.uk>
	<4DBF04E4.8020806@aon.at>
Message-ID: <4DBFE206.3030708@statistik.tu-dortmund.de>



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