[Rd] R CMD build then check fails on R-devel due to serialization version

luke-tierney at uiowa.edu luke-tierney at uiowa.edu
Thu Jan 11 14:47:49 CET 2018

As things stand now, package tarballs with vignettes that are built
with R-devel will not install in R 3.4.x, so CRAN can't accept them
and someone running R CMD check --as-cran should be told that. A
WARNING is appropriate.

Most likely what will change soon is that build/version.rds will be
saved with serialization version = 2 and this warning will not be
triggered just by having a vignette. It will still be triggered by
data files serialized with R-devel's default version = 3.

Please do remember that the 'devel' in R-devel means exactly that:
things will at times be unstable. There are currently a lot of balls
flying around with changes in R-devel and also Biocontuctor, and the
CRAN maintainers are working hard to keep things all up in the
air. Please be patient.



On Thu, 11 Jan 2018, Jim Hester wrote:

> This change poses difficulties for automated build systems such as
> travis-ci, which is widely used in the R community. In particular
> because this is a WARNING and not a NOTE this causes all R-devel
> builds with vignettes to fail, as the default settings fail the build
> if R CMD check issues a WARNING.
> The simplest change would be for R-core to change this message to be a
> NOTE rather than a WARNING, the serialization could still be tested
> and there would be a check against vignettes built with R-devel, but
> it would not cause these builds to fail.
> On Wed, Jan 10, 2018 at 3:52 PM, Duncan Murdoch
> <murdoch.duncan at gmail.com> wrote:
>> On 10/01/2018 1:26 PM, Neal Richardson wrote:
>>> Hi,
>>> Since yesterday I'm seeing `R CMD check --as-cran` failures on the
>>> R-devel daily build (specifically, R Under development (unstable)
>>> (2018-01-09 r74100)) for multiple packages:
>>> * checking serialized R objects in the sources ... WARNING
>>> Found file(s) with version 3 serialization:
>>> ‘build/vignette.rds’
>>> Such files are only readable in R >= 3.5.0.
>>> Recreate them with R < 3.5.0 or save(version = 2) or saveRDS(version =
>>> 2) as appropriate
>>> As far as I can tell, revision 74099
>>> (https://github.com/wch/r-source/commit/d9530001046a582ff6a43ca834d6c3586abd0a97),
>>> which changes the default serialization format to 3, clashes with
>>> revision 73973
>>> (https://github.com/wch/r-source/commit/885764eb74f2211a547b13727f2ecc5470c3dd00),
>>> which checks that serialized R objects are _not_ version 3. It seems
>>> that with the current development version of R, if you `R CMD build`
>>> and then run `R CMD check --as-cran` on the built package, it will
>>> fail.
>> I think the message basically says:  don't do that.  You should build with
>> R-release for now.  You always need to check with R-devel, so life is
>> complicated.
>> If you build with R-devel without forcing the old format, nobody using
>> R-release will be able to use your tarball.
>> Eventually I guess the new format will be accepted by CRAN, but it will
>> likely be a while:  nobody expects everyone to instantly upgrade to a new R
>> release, let alone to an unreleased development version.
>> Presumably that particular file (build/vignette.rds) could be automatically
>> built in the old format for now, but the new format needs testing, so it
>> makes sense to me to leave it as a default, even if it makes it more
>> complicated to submit a package to CRAN.
>> Duncan Murdoch
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu

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