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

cstrato cstrato at aon.at
Sun May 1 22:10:55 CEST 2011 

Dear Duncan, dear Uwe,

Since I have installed both WinXP and OpenSUSE 11.3 on my Mac in a 
virtual machine, I have now done the following tests on all three 
architectures:

1, R CMD build xps:
This creates "xps_1.13.1.tar.gz" which DOES contain all vignettes as 
pdf-file. Thus R CMD build is ok.

2, R CMD check xps:
This does NOT build the vignettes as pdf-files on all three 
architectures. Or to be more precise, R-2.13.0 does no longer build the 
vignettes since with R-2.12.2 and earlier versions R did create the 
vignettes as pdf-files.

Thus the question is:
Why does R CMD check no longer create the vignettes?

Best regards
Christian


On 4/27/11 10:16 AM, Uwe Ligges wrote:
>
>
> On 26.04.2011 21:58, cstrato wrote:
>> Dear Duncan, dear Uwe,
>>
>> Just now I have re-run everything, and today xps.Rnw can be converted to
>> a vignette w/o any problems using:
>> a, buildVignettes("xps", dir="/Volumes/CoreData/CRAN/xps", quiet=F)
>> b, R CMD Sweave xps.Rnw
>>
>> In both cases the vignette xps.pdf is created (maybe my Mac did not like
>> to work during eastern holidays).
>>
>> However, one issue remains:
>> "R64 CMD check xps_1.13.1.tar.gz" no longer creates any pdf files for
>> the vignettes.
>
>
> Dioes it give an error or warning? It should check the code. R CMD build
> creates the pdf files.
>
> Uwe Ligges
>
>>
>> Best regards
>> Christian
>>
>>
>> On 4/25/11 9:31 PM, Duncan Murdoch wrote:
>>> On 25/04/2011 3:16 PM, cstrato wrote:
>>>> Thank you.
>>>>
>>>> My problem seems to be that at the moment the problem can be seen only
>>>> on my Mac, since e.g. the Bioconductor servers have no problems
>>>> creating
>>>> the vignettes.
>>>
>>> Then you are definitely the one in the best position to diagnose the
>>> problem. Use the usual approach: simplify it by cutting out everything
>>> that looks unrelated. Verify that the problem still exists, then cut
>>> some more. Eventually you'll have isolated the error to a particular
>>> small snippet of code, and then you can add print() statements, or use
>>> trace(), or do whatever is necessary to see what's so special about your
>>> system.
>>>
>>> I suspect it will turn out to be an assumption in the code that is not
>>> true on your system.
>>>
>>> If the assumption is being made by code you wrote, then fix it. If it's
>>> being made by R, let us know.
>>>
>>> Duncan Murdoch
>>>
>>>>
>>>> Best regards
>>>> Christian
>>>>
>>>> On 4/25/11 8:55 PM, Duncan Murdoch wrote:
>>>>> cstrato wrote:
>>>>>> Dear Duncan,
>>>>>>
>>>>>> Thank you for your example, however it is different since it does not
>>>>>> use x and y. What about print(x+y)?
>>>>>
>>>>> Try it.
>>>>>
>>>>>>
>>>>>> Sorry, I do not believe that there is a bug in my code, since:
>>>>>> 1, it worked in all versions from R starting with R-2.6.0 till
>>>>>> R-2.12.2.
>>>>>> 2, the identical code works in the examples
>>>>>> 3, this code (or a similar code) is the starting code which all users
>>>>>> of xps have to use, and there was never a problem.
>>>>>
>>>>> This might be a problem in R, or might be a problem in your code. As
>>>>> far
>>>>> as I know, it has only shown up in your code, so I'd guess that's
>>>>> where
>>>>> the problem is. In any case, you're the one in the best position to
>>>>> isolate it and debug it.
>>>>>
>>>>> If it turns out to be a problem in R, put together an example
>>>>> illustrating the problem that doesn't involve your code, and I'll
>>>>> take a
>>>>> look.
>>>>>
>>>>> Duncan Murdoch
>>>>>
>>>>>>
>>>>>> Maybe the reason could be that my code has to import
>>>>>> - the CEL-files from the package dir
>>>>>> - the file SchemeTest3.root from the package dir
>>>>>> ??
>>>>>>
>>>>>> Best regards
>>>>>> Christian
>>>>>>
>>>>>> On 4/25/11 8:00 PM, Duncan Murdoch wrote:
>>>>>>> cstrato wrote:
>>>>>>>> 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.
>>>>>>> I'm either misreading what you wrote, or it's wrong. If I have this
>>>>>>> in a
>>>>>>> Sweave file:
>>>>>>>
>>>>>>> <<>>=
>>>>>>> x<- 1
>>>>>>> @
>>>>>>>
>>>>>>> <<>>=
>>>>>>> y<- 2
>>>>>>> @
>>>>>>>
>>>>>>> <<>>=
>>>>>>> print(x)
>>>>>>> @
>>>>>>>
>>>>>>> I will see the value of x getting printed, even though it came from
>>>>>>> two
>>>>>>> chunks earlier.
>>>>>>>
>>>>>>> I think Uwe is right: there is some bug in the code you're running.
>>>>>>> Sweave isn't the problem.
>>>>>>>
>>>>>>> Duncan Murdoch
>>>>>>>
>>>>>>>> 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
>>>>>>>> ______________________________________________
>>>>>>>> R-devel at r-project.org mailing list
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>>>
>>>>>
>>>>>
>>>
>>>
>

More information about the R-devel mailing list