I posted three files to http://astro.temple.edu/~rmh/HH-test/
HH_3.1-17.tar.gz ## my development version of HH. 00check-HH-R-3.1.2.log ## it passes R-3.1.2 cleanly 00check-HH-r68399.log ## many messages that I don't understand. Some of them I believe are reflections of the packages I depend or import or suggest. Thanks Rich On Mon, May 25, 2015 at 1:30 PM, Uwe Ligges <lig...@statistik.tu-dortmund.de> wrote: > > > On 25.05.2015 19:28, Richard M. Heiberger wrote: >> >> I will send it. what is the best way? direct to you? posting it on my >> website? > > > Website so others can look at it as well? > > Best, > Uwe > > >> >> On Mon, May 25, 2015 at 1:21 PM, Uwe Ligges >> <lig...@statistik.tu-dortmund.de> wrote: >>> >>> >>> >>> On 25.05.2015 18:59, Richard M. Heiberger wrote: >>>> >>>> >>>> I am still working on your suggestions. While doing so I found a more >>>> general concern. >>>> >>>> I am now trapped in incompatible circular dependencies. I don't know >>>> how to resolve them. >>>> >>>> The immediate specific is that ggplot2::layer and latticeExtra::layer >>>> are incompatible. >>>> >>>> Due to these dependencies I don't think I have control over which one >>>> has precedence. >>> >>> >>> >>> You have: import selectively from these packages using importFrom() >>> directives rather than simple import(). So you only import the layer >>> version >>> you actually need in your package (if any). >>> Try to get rid of Depends and solve all dependenciy issues via imports, >>> i.e. >>> NAMESPACE directives, where possible. >>> >>> >>>> I depend on lattice and latticeExtra and gridExtra. >>>> I import Hmisc and Rcmdr >>>> >>>> Hmisc Depends: lattice and ggplot2 >>>> Imports: latticeExtra, gridExtra >>>> >>>> gridExtra suggests ggplot2 and lattice >>>> >>>> Rcmdr imports abind, >>>> suggests e1071, Hmisc >>>> >>>> The message I am seeing with HH (which I cannot interpret by myself) >>>> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), >>>> versionCheck = vI[[j]]) : >>>> there is no package called 'abind' >>>> seems to be a consequence of importing Rcmdr. >>>> Since I do have this package the message is confusing at best. Can >>>> you rephrase the message? >>> >>> >>> >>> Perhaps a bug in another package? ANyway, can you give us the HH version >>> that triggers these problems? >>> >>> >>>> Perhaps by listing which specific line in which file is triggering it. >>>> >>>> I also sometime get a similar complaint about e1071 which I don't use >>>> at all but is suggested by Rcmdr. >>> >>> >>> >>> If a function in e1071 that needs it is called from a function in your >>> package, you may need to suggest it as well. >>> >>> >>>> I also get a complaint about TeachingDemos, which I have but don't use >>>> in HH. I haven't spotted >>>> where that dependency is coming from. However I see that >>>> TeachingDemos suggests both lattice and ggplot2. >>> >>> >>> >>> Don't know, again, I'd need the full package in order to say more. >>> >>> Best, >>> Uwe >>> >>> >>> >>>> Rich >>>> >>>> On Mon, May 25, 2015 at 3:44 AM, Uwe Ligges >>>> <lig...@statistik.tu-dortmund.de> wrote: >>>>> >>>>> >>>>> Two ideas: >>>>> >>>>> 1. Solve the first error at first: >>>>> >>>>> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), >>>>> versionCheck = >>>>> vI[[j]]) : >>>>> there is no package called 'abind' >>>>> Error: package or namespace load failed for 'HH' >>>>> Execution halted >>>>> >>>>> Looks like you forgot to declare abind as an Imports in your >>>>> DESCRIPTION >>>>> file? >>>>> >>>>> >>>>> 2. If you still get the other problems, please make a version of your >>>>> package available so that someone else can check and debug this. >>>>> >>>>> Best, >>>>> Uwe Ligges >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 25.05.2015 05:01, Richard M. Heiberger wrote: >>>>>> >>>>>> >>>>>> >>>>>> The problem is still there. I am working on both Windows and >>>>>> Macintosh. >>>>>> >>>>>> The packages I have check clean using R-3.1.2 on Windows. >>>>>> They "INSTALL --build" and "build" using 3.3.0-devl on Windows and >>>>>> 3.2.0 >>>>>> on Mac, >>>>>> >>>>>> I downloaded R-devel for Windows this afternoon and updated to >>>>>> Rtools33. >>>>>> I have attached two R CMD check log files with this combination >>>>>> * using R Under development (unstable) (2015-05-22 r68399) >>>>>> * using platform: i386-w64-mingw32 (32-bit) >>>>>> >>>>>> >>>>>> The 3.1-15 is the version currently on CRAN. >>>>>> It complains it can't find Hmisc. Hmisc is installed. >>>>>> The built package inside the Rcheck directory loads. >>>>>> Package check results on CRAN don't show this warning. >>>>>> >>>>>> >>>>>> The 3.1-17 is the version I am working on. >>>>>> It complains it can't find abind. abind is installed. >>>>>> It gives 6 versions of this message. >>>>>> Error in validObject(.Object) : >>>>>> invalid class "ObjectsWithPackage" object: superclass >>>>>> "atomicVector" >>>>>> not defined in the environment of the object's class >>>>>> I don't understand what is triggering them. >>>>>> The built package inside the Rcheck directory loads. >>>>>> >>>>>> On Sat, May 23, 2015 at 9:02 AM, Uwe Ligges >>>>>> <lig...@statistik.tu-dortmund.de> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> Can you try a more recent version of R-devel with all relevant >>>>>>> packages >>>>>>> you >>>>>>> depend on re-installed? >>>>>>> >>>>>>> Looks like either a bug in that months old version of R-devel or an >>>>>>> inconsistancy of installed packages and the version of the methods >>>>>>> package >>>>>>> or so. >>>>>>> >>>>>>> Best, >>>>>>> Uwe Ligges >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 23.05.2015 05:29, Richard M. Heiberger wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> followup. >>>>>>>> >>>>>>>> I backed up to R-3.1.2 and fixed the problems it found. >>>>>>>> Then I tried again with R-3.2.0 and I am still getting these >>>>>>>> messages >>>>>>>> >>>>>>>> Error in validObject(.Object) : >>>>>>>> invalid class "ObjectsWithPackage" object: superclass >>>>>>>> "atomicVector" >>>>>>>> not defined in the environment of the object's class >>>>>>>> Calls: <Anonymous> ... metaNameUndo -> new -> initialize -> >>>>>>>> initialize >>>>>>>> -> validObject >>>>>>>> Execution halted >>>>>>>> >>>>>>>> On Fri, May 22, 2015 at 8:08 PM, Richard M. Heiberger >>>>>>>> <r...@temple.edu> >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> I am updating the HH package and have series of messages that I >>>>>>>>> don't >>>>>>>>> recognize. >>>>>>>>> >>>>>>>>> bash-3.2$ R CMD check HH2 >>>>>>>>> * using log directory >>>>>>>>> '/Users/rmh/WindowsC/HOME/rmh/HH-R.package/HH2.Rcheck' >>>>>>>>> * using R Under development (unstable) (2015-02-12 r67812) >>>>>>>>> * using platform: x86_64-apple-darwin13.4.0 (64-bit) >>>>>>>>> * using session charset: ASCII >>>>>>>>> * checking for file 'HH2/DESCRIPTION' ... OK >>>>>>>>> * checking extension type ... Package >>>>>>>>> * this is package 'HH' version '3.1-17' >>>>>>>>> * checking package namespace information ... OK >>>>>>>>> * checking package dependencies ... OK >>>>>>>>> * checking if this is a source package ... OK >>>>>>>>> * checking if there is a namespace ... OK >>>>>>>>> * checking for executable files ... OK >>>>>>>>> * checking for hidden files and directories ... NOTE >>>>>>>>> Found the following hidden files and directories: >>>>>>>>> .DS_Store >>>>>>>>> inst/.DS_Store >>>>>>>>> These were most likely included in error. See section 'Package >>>>>>>>> structure' in the 'Writing R Extensions' manual. >>>>>>>>> * checking for portable file names ... OK >>>>>>>>> * checking for sufficient/correct file permissions ... OK >>>>>>>>> * checking whether package 'HH' can be installed ... OK >>>>>>>>> * checking installed package size ... OK >>>>>>>>> * checking package directory ... OK >>>>>>>>> * checking DESCRIPTION meta-information ... OK >>>>>>>>> * checking top-level files ... OK >>>>>>>>> * checking for left-over files ... OK >>>>>>>>> * checking index information ... OK >>>>>>>>> * checking package subdirectories ... OK >>>>>>>>> * checking R files for non-ASCII characters ... OK >>>>>>>>> * checking R files for syntax errors ... OK >>>>>>>>> * checking whether the package can be loaded ... OK >>>>>>>>> * checking whether the package can be loaded with stated >>>>>>>>> dependencies >>>>>>>>> ... >>>>>>>>> OK >>>>>>>>> * checking whether the package can be unloaded cleanly ... OK >>>>>>>>> * checking whether the namespace can be loaded with stated >>>>>>>>> dependencies >>>>>>>>> ... OK >>>>>>>>> * checking whether the namespace can be unloaded cleanly ... OK >>>>>>>>> * checking dependencies in R code ... NOTE >>>>>>>>> Error in validObject(.Object) : >>>>>>>>> invalid class "ObjectsWithPackage" object: superclass >>>>>>>>> "atomicVector" >>>>>>>>> not defined in the environment of the object's class >>>>>>>>> Execution halted >>>>>>>>> >>>>>>>>> I have two questions about it. >>>>>>>>> 1. What is it checking? There are no words in the message that >>>>>>>>> indicate which of my >>>>>>>>> functions is being looked at. >>>>>>>>> >>>>>>>>> I am getting 6 of these. They are all identically worded. >>>>>>>>> sometimes >>>>>>>>> they are >>>>>>>>> NOTE ERROR WARNING >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Rich >>>>>>>>> >>>>>>>>> 2. How can I run R CMD check, or its components, in a way that will >>>>>>>>> stop >>>>>>>>> and >>>>>>>>> let me investigate from the point? I am looking for the equivalent >>>>>>>>> of >>>>>>>>> the R option >>>>>>>>> option(error=recover) >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ______________________________________________ >>>>>>>> R-package-devel@r-project.org mailing list >>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel >>>>>>>> >>>>>>> >>>>> >>> > ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
