From cstrato at aon.at  Tue May  3 21:14:47 2011
From: cstrato at aon.at (cstrato)
Date: Tue, 03 May 2011 21:14:47 +0200
Subject: [Rd] How to create vignette.pdf for R-2.13.0?
In-Reply-To: <4DBFE206.3030708@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>	<4DB5AFD4.9020303@aon.at>
	<4DB5B6B0.90607@gmail.com>	<4DB5C286.40306@aon.at>
	<4DB5C38D.6030400@gmail.com>	<4DB5C87C.5040905@aon.at>
	<4DB5CBFD.6050508@gmail.com>	<4DB723F9.7090800@aon.at>	<4DB7D0DD.6040201@statistik.tu-dortmund.de>	<4DBDBE4F.8020702@aon.at>
	<4DBDEA8F.60000@gmail.com>	<alpine.LFD.2.02.1105020549360.441@gannet.stats.ox.ac.uk>
	<4DBF04E4.8020806@aon.at>
	<4DBFE206.3030708@statistik.tu-dortmund.de>
Message-ID: <4DC05427.7060908@aon.at>

Dear Uwe,

This is my development cycle:

First, I run R CMD check until there are no more warnings/errors. Since 
years it was very convenient that R CMD check builds the pdf-files of 
the vignettes, too, since this allowed me to correct errors in the 
manual files and the vignette files at the same time!

Afterwards I run R CMD INSTALL to install my package and do more tests 
until everything works.

As you see I do not use R CMD build, since every run takes about 5 
minutes, it overwrites my zipped source code, and I would need to unzip 
it to get access to the vignette pdf-files.

Best regards
Christian


On 5/3/11 1:07 PM, Uwe Ligges wrote:
>
>
> On 02.05.2011 21:24, cstrato wrote:
>> Dear Prof. Ripley,
>>
>> Thank you for your confirmation and explanation, I understand the reason
>> for cleaning things up to save memory. However, it was very convenient
>> to have this feature in earlier versions of R. It would be really
>> helpful to have an additional option to R CMD check, e.g.
>> "--no-clean-vignettes".
>>
>> FYI, I did not claim "..create the vignettes *in <pkg>inst/doc*",
>> instead my words were:
>> One interesting observation is that xps.Rcheck from R-2.12.2 contains
>> the subdirectory "inst/doc" with the vignettes while xps.Rcheck from
>> R-2.13.0 does not contain "inst".
>
>
> But you do not need it. I do not know how often I have to mention that
> vignettes are produced by R CMD build! They are already build when
> running R CMD check. And please do not tell us about tzhe PDF version
> oif manuals which are *unrelated* to vignettes, because they are not
> built in advance and need to be checked, since they should be produced
> at user level while vignettes are built at developer level already.
>
> Uwe Ligges
>
>
>> 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
>> _._._._._._._._._._._._._._._._._._
>>
>>
>> On 5/2/11 7:08 AM, Prof Brian Ripley wrote:
>>> On Sun, 1 May 2011, Duncan Murdoch wrote:
>>>
>>>> On 11-05-01 4:10 PM, cstrato wrote:
>>>>> 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?
>>>>
>>>> Probably the answer is simply "because it doesn't". For a truly
>>>> reliable check, you should build the package, then check the tar.gz
>>>> file. Anything else is, and always has been, an approximation.
>>>
>>> Actually, it does. What earlier versions never did (despite 'cstrato's
>>> repeated delusional claims earlier) was to create the vignettes *in
>>> <pkg>inst/doc*. All of them re-created (by default) vignettes in a
>>> working directory. The difference is that 2.13.0 deletes that working
>>> directory if the test was successful, whereas earlier versions left the
>>> results somewhere in <pkg>.Rcheck (the 'somewhere' has varied). However,
>>> earier versions of R CMD check sometimes failed when R CMD build
>>> succeeded
>>>
>>> Using Animal (a small CRAN package with one vignette).
>>>
>>> R 2.12.2 gave
>>>
>>> * checking package vignettes in ?inst/doc? ... WARNING
>>> Package vignettes without corresponding PDF:
>>> /tmp/Animal/inst/doc/Animal.Rnw
>>>
>>> and the vignette was re-created in Animal.Rcheck/inst/doc.
>>>
>>> R 2.13.0 gives
>>>
>>> * checking package vignettes in ?inst/doc? ... WARNING
>>> Package vignette(s) without corresponding PDF:
>>> Animal.Rnw
>>>
>>> Non-ASCII package vignette(s) without specified encoding:
>>> Animal.Rnw
>>>
>>> * checking running R code from vignettes ... OK
>>> * checking re-building of vignettes ... OK
>>>
>>> and the working directory was Animal.Rcheck/vign_test .
>>>
>>> The main reason for cleaning up is that to mimic R CMD build the test
>>> has to make a complete copy of the package sources, and that adds up:
>>> checking CRAN already takes 17GB for each flavour.
>>>
>>>
>>>>
>>>> Duncan Murdoch
>>>>
>>>>
>>>>>
>>>>> 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
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>>>> ______________________________________________
>>>> 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