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.kepplin...@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.ga...@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.kepplin...@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.kepplin...@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.turg...@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-boun...@r-project.org> on >> > >> behalf of David Kepplinger <david.kepplin...@gmail.com> >> > >> *Sent:* March 13, 2019 3:39 PM >> > >> *To:* r-package-devel@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@r-project.org mailing list >> > >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >> > >> >> > > >> > >> > [[alternative HTML version deleted]] >> > >> > ______________________________________________ >> > R-package-devel@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/r-package-devel ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel