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

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 at 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 at 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 at 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 at test.com.au>
Maintainer: Rob Foxall <rob.foxall at 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 at test.com>
Maintainer:  <rob.foxall at 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 at 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 at 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.

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