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

[Uwe Ligges]

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.



> Using R CMD check with R-2.12.2 I get:

I thought we are talking about R-2.13.0?

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?
>
> 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.


> 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?

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
>>
>
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