[R-pkg-devel] R CMD build: "Error in if (any(update))"

[Uwe Ligges]

Too many layers of complexity for me, can you take the package sources 
and zat /or zip) them for me and send them? Then I'll take a look.
Best,
Uwe Ligges

On 12.06.2019 08:23, Rob Foxall wrote:
> Thanks. I ran in R:
> devtools::build("myPackage")
> That gave me a warning:
>       NB: this package now depends on R (>= 3.5.0)
>       WARNING: Added dependency on R >= 3.5.0 because serialized
> objects in  serialize/load version 3 cannot be read in older versions
> of R.
>       File(s) containing such objects: 'myPackage/R/sysdata.rda'
> 'myPackage/data/myCol.rda'
> But it didn't error. I then added the dependency to R >= 3.5.0 to my
> DESCRIPTION file, and rerunning devtools::build now executed without
> error or warning. However, in the command window "R CMD build
> myPackage" still gives same error.
> Then in R I ran:
> devtools::check("myPackage")
> It gave me a genuine error ("myplot" instead of "myPlot" in my
> myPackage-package.rda file), and a couple of warnings. All of which I
> fixed, and re-running the check gave me 0 errors/warnings/notes.
> In the command window, "R CMD build myPackage" still gives the same error.
> 
> On Wed, Jun 12, 2019 at 12:46 PM David Hugh-Jones
> <davidhughjones using gmail.com> wrote:
>>
>> If you use devtools::check, I think it runs in the original R process, so you might be able to debug the error using eg options(error=recover).
>>
>> On Wed, 12 Jun 2019 at 02:31, Rob Foxall <rfoxall27 using gmail.com> wrote:
>>>
>>> Thanks for the replies. I am still stuck, although agree it is most
>>> likely due to change to R version 3.6.0. I did however manage to
>>> create a dummy package that now does re-create the same error, this
>>> required the inclusion of a data object. The R CMD build error occurs
>>> regardless of whether there is a sysdata.rda in the R subdirectory,
>>> and whether there is a datalist in the data subdirectory. Apologies
>>> for the lengthy "code" that follows:
>>>
>>> In R:
>>> myCol <- rgb(0.9,0.5,0.5)
>>> myPlot <- function(x){
>>>     plot(x, col = myCol)
>>>     return(NULL)
>>> }
>>> package.skeleton(name = "myPackage", list = c("myPlot", "myCol"))
>>>
>>> "Optionally" in R:
>>> save(list = c("myCol"), file = "sysdata.rda")
>>>
>>> my DESCRIPTION file:
>>> Package: myPackage
>>> Type: Package
>>> Title: Test Package
>>> Version: 1.0
>>> Date: 2019-06-11
>>> Author: Rob Foxall <rob.foxall using test.com.au>
>>> Maintainer: Rob Foxall <rob.foxall using test.com.au>
>>> Description: To test making a package
>>> License: GPL-2
>>> LazyLoad: yes
>>>
>>> my NAMESPACE file:
>>> exportPattern("^[[:alpha:]]+")
>>>
>>> contents of myPackage directory:
>>> directories "data", "man", "R", files "DESCRIPTION", "NAMESPACE",
>>> "Read-and-delete-me"
>>> contents of data subdirectory:
>>> myCol.rda, (optionally) datalist
>>> contents of man subdirectory:
>>> myCol.Rd, myPackage-package.Rd, myPlot.Rd
>>> contents of R subdirectory:
>>> myPlot.R, ("optionally") sysdata.rda
>>>
>>> The ".Rd" files:
>>> myCol.Rd:
>>> \name{myCol}
>>> %
>>> \alias{myCol}
>>> %
>>> \docType{data}
>>> %
>>> \title{A colour}
>>> %
>>> \description{It's a colour}
>>> %
>>> \usage{data(myCol)}
>>> %
>>> \format{
>>> It is a colour, defined by:
>>> rgb(red=0.9,green=0.5,blue=0.5)
>>> }
>>> %
>>> \details{
>>> Other, standard colours are available via sensible names. See \code{colours}. }
>>> %
>>> \source{See Me}
>>> %
>>> \references{Albers, J. (1975) \emph{Interaction of Colour}. Yale
>>> University Press}
>>> %
>>> \examples{
>>> myPlot(3)
>>> }
>>> %
>>> \keyword{sysdata}
>>>
>>> myPackage-package.Rd:
>>> \name{myPackage-package}
>>> %
>>> \alias{myPackage-package}
>>> %
>>> \alias{myPackage}
>>> %
>>> \docType{package}
>>> %
>>> \title{Test package}
>>> %
>>> \description{Testing making a package}
>>> %
>>> \details{
>>> \tabular{ll}{
>>> Package: \tab myPackage\cr
>>> Type: \tab Package\cr
>>> Version: \tab 1.0\cr
>>> Date: \tab 2019-06-11\cr
>>> License: \tab GPL-2\cr
>>> LazyLoad: \tab yes\cr
>>> }
>>> %
>>> Test package, dummy plot with dummy colour
>>> }
>>> %
>>> \author{
>>> Rob Foxall <rob.foxall using test.com>
>>> Maintainer:  <rob.foxall using test.com>
>>> }
>>> %
>>> \references{N.A.J. Hastings, Brian Peacock, Merran Evans (2000)
>>> \emph{Statistical Distributions} John Wiley & Sons Inc}
>>> %
>>> \keyword{package}
>>> %
>>> \seealso{\code{\link{plot}}}
>>> %
>>> \examples{
>>> myplot(3)
>>> }
>>>
>>> myPlot.Rd
>>> \name{myPlot}
>>> %
>>> \alias{myPlot}
>>> %- Also NEED an '\alias' for EACH other topic documented here.
>>> \title{Do a plot of a number}
>>> %
>>> \description{Plots a number with a set colour}
>>> %
>>> \usage{myPlot(x)}
>>> %
>>> \arguments{
>>>    \item{x}{A number}
>>> }
>>> %
>>> \details{Plots a number with a colour.}
>>> %
>>> \value{Returns null}
>>> %
>>> \author{Rob Foxall}
>>> %
>>> \note{There is no note}
>>> %
>>> \seealso{\code{\link{plot}}}
>>> %
>>> \examples{myPlot(3)}
>>> %
>>> \keyword{KPI}
>>>
>>>
>>> On Tue, Jun 11, 2019 at 12:00 AM William Dunlap <wdunlap using tibco.com> wrote:
>>>>
>>>> You might be able to find where the error occurred by putting the following lines in ~/.Rprofile
>>>>
>>>> cat("~/.Rprofile: setting alternate error handler\n")
>>>> options(
>>>>      error=quote({
>>>>          dump.frames()
>>>>          writeLines(c("Stack trace", paste0("  ",names(last.dump))))}))
>>>>
>>>> Bill Dunlap
>>>> TIBCO Software
>>>> wdunlap tibco.com
>>>>
>>>>
>>>> On Mon, Jun 10, 2019 at 6:38 AM Rob Foxall <rfoxall27 using gmail.com> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> (Re-posting here as per advice from r-help)
>>>>>
>>>>> I've got an R package that I periodically create in what I assume is
>>>>> an old-fashioned way:
>>>>>
>>>>> Within R: use "package.skeleton"
>>>>> Outside of R: update e.g. .rd files as appropriate
>>>>> Command window: run the following commands
>>>>> R CMD build packageName
>>>>> R CMD check packageName
>>>>> R CMD INSTALL --build packageName
>>>>>
>>>>> I am now getting an error on the R CMD build stage. Initially I had
>>>>> wanted to remove a package dependency (by not passing some functions
>>>>> to package.skeleton and editing my NAMESPACE and DESCRIPTION file
>>>>> appropriately), but on getting the error I tried to revert everything
>>>>> back to my last successful build (Feb 2019), however, the error
>>>>> persisted:
>>>>> R CMD build packageName
>>>>> * checking for file 'packageName/DESCRIPTION' ... OK
>>>>> * preparing 'packageName' :
>>>>> * checking DESCRIPTION meta-information ... OK
>>>>> * checking for LF line-endings in source and make files
>>>>> * checking for empty or unneeded directories
>>>>> * looking to see if a 'data/datalist' file should be added
>>>>> Error in if (any(update)) { : missing value where TRUE/FALSE needed
>>>>> Execution halted
>>>>>
>>>>> I am guessing that the error could be due to any of the last three
>>>>> lines that don't have an "OK", but I am completely stuck as to how to
>>>>> narrow it down further, and Dr. Google has already failed me.
>>>>>
>>>>> Using R version 3.6.0, R tools version 3.5.0.4 (I don't recall if had
>>>>> different versions previous time I built this package in Feb 2019).
>>>>> Attempt to reproduce error with dummy package failed (i.e. no issues
>>>>> with R CMD build).
>>>>>
>>>>> Cheers,
>>>>> Rob.
>>>>>
>>>>> ______________________________________________
>>>>> R-package-devel using r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>> ______________________________________________
>>> R-package-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>> --
>> Sent from Gmail Mobile
> 
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