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

[luke-tierney at uiowa.edu]

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.

Best,

luke

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
>>
>>
>> ______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
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> 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