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

Duncan Murdoch murdoch.duncan at gmail.com
Mon Apr 25 20:00:16 CEST 2011 

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
> 
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