[R-pkg-devel] R CMD build: "Error in if (any(update))"
Rob Foxall
r|ox@||27 @end|ng |rom gm@||@com
Wed Jun 12 15:31:06 CEST 2019
Thanks so much for looking into this. You were right, my path that I
had been too lazy to update was pointing at an older installation of R
that I had been too lazy to uninstall.
On Wed, Jun 12, 2019 at 6:41 PM Uwe Ligges
<ligges using statistik.tu-dortmund.de> wrote:
>
> So this is likely caused by your setup as I simply get
>
> $ R CMD build myPackage
> * checking for file 'myPackage/DESCRIPTION' ... OK * preparing 'myPackage':
> * checking DESCRIPTION meta-information ... OK
> * checking for LF line-endings in source and make files and shell scripts
> * checking for empty or unneeded directories
> * looking to see if a 'data/datalist' file should be added
> * building 'myPackage_1.0.tar.gz'
>
>
> Best,
> Uwe Ligges
>
>
>
>
>
>
> On 12.06.2019 10:54, Rob Foxall wrote:
> > Thank you, that is very kind. zip attached. As best as I can see the
> > summary is that there are no issues building/checking when done
> > internally in R session using devtools; but running command window "R
> > CMD build myPackage" fails.
> >
> > Cheers,
> > Rob.
> >
> > On Wed, Jun 12, 2019 at 4:29 PM Uwe Ligges
> > <ligges using statistik.tu-dortmund.de> wrote:
> >>
> >> 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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> >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>>
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