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

Duncan Murdoch murdoch.duncan at gmail.com
Mon Apr 25 21:31:09 CEST 2011 

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
>>>>
>>
>>

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