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.ga...@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.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 > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
