R devel - Jan 2018 - R CMD build then check fails on R-devel due to serialization version

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.

Neal

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

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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