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

From: Uwe Ligges <ligges_at_statistik.tu-dortmund.de>
Date: Mon, 25 Apr 2011 16:00:26 +0200

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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