From cstrato at aon.at  Mon Apr 25 19:31:00 2011
From: cstrato at aon.at (cstrato)
Date: Mon, 25 Apr 2011 19:31:00 +0200
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
In-Reply-To: <4DB57E7A.1080507@statistik.tu-dortmund.de>
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>
Message-ID: <4DB5AFD4.9020303@aon.at>

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.

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
>>>
>



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