From cstrato at aon.at  Sun Apr 24 20:59:04 2011
From: cstrato at aon.at (cstrato)
Date: Sun, 24 Apr 2011 20:59:04 +0200
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
In-Reply-To: <4DB42FB3.9090401@statistik.tu-dortmund.de>
References: <4DB32D9F.5010406@aon.at>
	<4DB42FB3.9090401@statistik.tu-dortmund.de>
Message-ID: <4DB472F8.9060903@aon.at>

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.

Using R CMD check with R-2.12.2 I get:

$ 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.

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.

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

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
>



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