No, I simply do "tar czf xps_1.13.1.tar.gz xps". Best regards Christian
On 5/3/11 11:11 PM, Simon Urbanek wrote: > On May 3, 2011, at 4:48 PM, cstrato<cstr...@aon.at> wrote: > >> Dear Uwe, >> >> Thank you, however since I use "R CMD INSTALL xps.tar.gz" my source code is >> not polluted. >> > > But then you already used build to create the tar ball so the vignette has > been built. So what is your point? > > Cheers, > S > > >> Furthermore, I forgot to mention that finally I upload the source code only >> to the BioC svn repository. The rest is done by the BioC servers, including >> building the pdf-files for the vignettes. >> >> Best regards >> Christian >> >> >> On 5/3/11 10:13 PM, Uwe Ligges wrote: >>> >>> >>> On 03.05.2011 21:14, cstrato wrote: >>>> 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. >>> >>> >>> Then this is the main problem here. The *recommended* development cycle >>> from the manuals is to run >>> >>> 1. R CMD build in order to get a valid source tarball and clean the sources >>> 2. R CMD INSTALL to check if your package can be installed >>> 3. R CMD check in order to finally check your package >>> >>> Running R CMD INSTALL on your source directory may pollute it, hence >>> this is not recommended at all. >>> >>> >>> Best, >>> UWe >>> >>> >>> >>> >>> >>>> >>>> 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@r-project.org mailing list >>>>>>>>>>>>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel >>>>>>>>>>>>>>>>>>>>> ______________________________________________ >>>>>>>>>>>>>>>>>>>>> R-devel@r-project.org mailing list >>>>>>>>>>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel >>>>>>>>>>>>>>>>> ______________________________________________ >>>>>>>>>>>>>>>>> R-devel@r-project.org mailing list >>>>>>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel >>>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>>>> ______________________________________________ >>>>>>>> R-devel@r-project.org mailing list >>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel >>>>>>>> >>>>>>> >>>>>> >>>>>> ______________________________________________ >>>>>> R-devel@r-project.org mailing list >>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel >>>>> >>> >> >> ______________________________________________ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel