[R-pkg-devel] CRAN incoming checks fail due to non-staged installation

[David Kepplinger]

Thanks, Gábor, for taking the time to investigate the issue and the
detailed elaboration!
I resubmitted to CRAN with a brief explanation and a link to this thread.

Thanks,
David

On Tue, Mar 26, 2019 at 2:55 PM Gábor Csárdi <csardi.gabor using gmail.com> wrote:

> OK, here is what I think is going on.
>
> There is a bug in the check code, that creates a false positive when
> the package installation is performed with `--merge-multiarch`. In
> this case the x64 architecture uses a non-staged install,
> deliberately, but the check code still picks this up and reports it as
> a NOTE.
>
> Reproducing it is not easy, because of several reasons:
> - win-builder uses package-specific configuration, in this case your
> package is listed in
>
> https://svn.r-project.org/R-dev-web/trunk/CRAN/QA/Uwe/make/config/MergeMultiarch
> ,
> so `--merge-multiarch` is added automatically.
> - R CMD check cannot pass --merge-multiarch to R CMD INSTALL because
> --merge-multiarch only works on tarballs, and R CMD check runs INSTALL
> on a directory.
> - However, R CMD check has an undocumented --install=... option, which
> can be used to pick up the installation output from a certain file. I
> am pretty sure that win-builder uses this. I.e. it calls R CMD INSTALL
> first, putting the output to a file, and then calls R CMD check with
> the --install= option pointing to that file as the install output.
>
> In summary, I think this an R CMD check bug, added in this commit:
>
> https://github.com/wch/r-source/commit/44e8faeb1ed30a7603e79988639da7e4e358d497
>
> It can be fixed easily by using a slightly different message for the
> --merge-multiarch case, or maybe even by not specifying
> --no-staged-install here:
>
> https://github.com/wch/r-source/blob/be469e86046389a0213f22e8b5c7b3227558bb01/src/library/tools/R/install.R#L1913
> and here:
>
> https://github.com/wch/r-source/blob/be469e86046389a0213f22e8b5c7b3227558bb01/src/library/tools/R/install.R#L1938
> because --libs-only implies --no-staged-install anyway. I am not
> entirely certain, but Tomas and/or Prof Ripley will know for sure.
>
> If you want submit your package before the bug is fixed, I suggest you
> explain this directly to CRAN when you submit your package.
>
> Best,
> Gabor
>
> On Tue, Mar 26, 2019 at 3:18 PM David Kepplinger
> <david.kepplinger using gmail.com> wrote:
> >
> > Dear Gábor,
> >
> > Oddly, it does emit a NOTE due to the non-staged install, as can be seen
> at https://win-builder.r-project.org/86i67mqTD9YY
> >
> > The package source can be found at
> https://github.com/dakep/pense-rpkg/tree/release/1.2.2
> >
> > Thanks for your help,
> > David
> >
> >
> > On Tue, Mar 26, 2019, 3:28 AM Gábor Csárdi, <csardi.gabor using gmail.com>
> wrote:
> >>
> >> Hi David,
> >>
> >> if you only see
> >>
> >> install for i386
> >> * installing *source* package 'pense' ...
> >> ** using staged installation
> >> [....]
> >> install for x64
> >> * installing *source* package 'pense' ...
> >> ** using non-staged installation
> >> [...]
> >>
> >> then everything is fine, there is no NOTE here, AFAICT.
> >>
> >> If you see a NOTE about this, please post 1) a link to your package,
> >> and 2) a link to the win-builder output.
> >>
> >> Thanks,
> >> Gabor
> >>
> >> On Tue, Mar 26, 2019 at 12:13 AM David Kepplinger
> >> <david.kepplinger using gmail.com> wrote:
> >> >
> >> > Dear Community,
> >> >
> >> > The issue persists and I don't know if it is something I can fix or
> if it's
> >> > a false positive from the CRAN incoming checks. As a result, the
> package is
> >> > archived as the old version has other issues with the new R version.
> >> >
> >> > Does someone have an idea how I can fix the issue? I have asked the
> CRAN
> >> > team last week to flag the issue as a false positive, but I haven't
> heard
> >> > back so I assume it's something I have to fix.
> >> >
> >> > Thanks,
> >> > David
> >> >
> >> > On Wed, Mar 13, 2019 at 3:34 PM David Kepplinger <
> david.kepplinger using gmail.com>
> >> > wrote:
> >> >
> >> > > Thank you, Max, for the clarification.
> >> > > I have added the option "StagedInstall: yes" to the DESCRIPTION
> file, but
> >> > > it doesn't seem to be forcing a staged installation for x64 on
> Windows. I
> >> > > get the same NOTE now from winbuilder, but with more explanation
> which
> >> > > could help isolate the problem:
> >> > >
> >> > > install for i386
> >> > > * installing *source* package 'pense' ...
> >> > > ** using staged installation
> >> > > [...]
> >> > > install for x64
> >> > > * installing *source* package 'pense' ...
> >> > > not using staged install with --libs-only
> >> > > ** using non-staged installation
> >> > > [...]
> >> > >
> >> > >
> >> > > Best,
> >> > > David
> >> > >
> >> > > On Wed, Mar 13, 2019 at 1:21 PM Maxime Turgeon <
> >> > > maxime.turgeon using mail.mcgill.ca> wrote:
> >> > >
> >> > >> Hi David,
> >> > >>
> >> > >> Non-staged installation is something new in R-devel:
> >> > >>
> https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html
> >> > >>
> >> > >>
> >> > >> Package maintainers can opt out of it (through DESCRIPTION), and
> I'm
> >> > >> assuming CRAN wants a quick way to know if that was the case when
> >> > >> diagnosing a submission.
> >> > >>
> >> > >> To resolutely opt *in* (which will eventually be the default), you
> could
> >> > >> try adding "StagedInstall: yes" to your DESCRIPTION file.
> >> > >>
> >> > >> Of course, one question still remains: why was the behaviour
> different
> >> > >> for the two architectures.
> >> > >>
> >> > >> Max
> >> > >> ------------------------------
> >> > >> *From:* R-package-devel <r-package-devel-bounces using r-project.org> on
> >> > >> behalf of David Kepplinger <david.kepplinger using gmail.com>
> >> > >> *Sent:* March 13, 2019 3:39 PM
> >> > >> *To:* r-package-devel using r-project.org
> >> > >> *Subject:* [R-pkg-devel] CRAN incoming checks fail due to
> non-staged
> >> > >> installation
> >> > >>
> >> > >> Dear Community,
> >> > >>
> >> > >> I am trying to update the pense package on CRAN to fix `autoreconf`
> >> > >> problems, but the incoming checks fail for Windows (r-devel) with
> 2 NOTEs.
> >> > >>
> >> > >> The first NOTE is a HTTP 403 for a http://doi.org URL which I
> already
> >> > >> know
> >> > >> about and can not change, but the other NOTE is more obscure to
> me. It
> >> > >> says
> >> > >>
> >> > >> * checking whether package 'pense' can be installed ... NOTE
> >> > >> Found the following notes/warnings:
> >> > >>   Non-staged installation was used
> >> > >>
> >> > >>
> >> > >> and when I check the install log, it says
> >> > >>
> >> > >> install for i386
> >> > >> * installing *source* package 'pense' ...
> >> > >> ** using staged installation
> >> > >> [....]
> >> > >> install for x64
> >> > >> * installing *source* package 'pense' ...
> >> > >> ** using non-staged installation
> >> > >> [...]
> >> > >>
> >> > >>
> >> > >> Is this a false positive or is there something I can do to force
> using a
> >> > >> staged installation for both architectures on Windows?
> >> > >>
> >> > >> Best,
> >> > >> David
> >> > >>
> >> > >>         [[alternative HTML version deleted]]
> >> > >>
> >> > >> ______________________________________________
> >> > >> R-package-devel using r-project.org mailing list
> >> > >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >> > >>
> >> > >
> >> >
> >> >         [[alternative HTML version deleted]]
> >> >
> >> > ______________________________________________
> >> > R-package-devel using r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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