From cstrato at aon.at  Mon Apr 25 20:50:46 2011
From: cstrato at aon.at (cstrato)
Date: Mon, 25 Apr 2011 20:50:46 +0200
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
In-Reply-To: <4DB5B6B0.90607@gmail.com>
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>
Message-ID: <4DB5C286.40306@aon.at>

Dear Duncan,

Thank you for your example, however it is different since it does not 
use x and y. What about print(x+y)?

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.

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
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>
>



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