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

Sun Apr 24 23:10:22 CEST 2011

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.

> 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?

>>
>> 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.

>
>> 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?

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
>>>
>>
>> ______________________________________________
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>