[R-pkg-devel] CRAN submission with warnings
Hi, What is the usual process to submit a new package to CRAN which has false-positive warnings? I submitted rtree_0.2.0 last week (7/21). This package compiles with warnings from Boost headers. The warnings are expected, unavoidable, and unimportant, which I documented in cran-comments.md. After submitting the package, I got an email that the package failed the pre-test due to the warnings. I replied-all, pointing to the explanation in cran-comments.md. I haven't heard anything since, and the package is still in the archive folder at ftp://cran.r-project.org/incoming. I'm new to this process. Is there something else I should do, or should I just sit tight and wait for a response? win-builder results are here: https://win-builder.r-project.org/incoming_pretest/rtree_0.2.0_20210721_153225/Windows/00check.log cran-comments.md here: https://github.com/akoyabio/rtree/blob/master/cran-comments.md Thank you for any guidance, Kent Johnson Akoya Biosciences [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] CRAN submission with warnings
Thanks Michael! So I should re-submit the package with the documentation on WARNINGS in the comments section of the submission? Kent From: Michael Dewey Sent: Monday, July 26, 2021 12:07 PM To: Kent Johnson ; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] CRAN submission with warnings Dear Kent I think the canonical way to report these is in the space on the submission form, unless I have not correctly grasped what you did. Michael On 26/07/2021 16:02, Kent Johnson wrote: > Hi, > > What is the usual process to submit a new package to CRAN which has > false-positive warnings? > > I submitted rtree_0.2.0 last week (7/21). This package compiles with warnings > from Boost headers. The warnings are expected, unavoidable, and unimportant, > which I documented in cran-comments.md. After submitting the package, I got > an email that the package failed the pre-test due to the warnings. I > replied-all, pointing to the explanation in cran-comments.md. I haven't heard > anything since, and the package is still in the archive folder at > ftp://cran.r-project.org/incoming<ftp://cran.r-project.org/incoming>. > > I'm new to this process. Is there something else I should do, or should I > just sit tight and wait for a response? > > win-builder results are here: > https://win-builder.r-project.org/incoming_pretest/rtree_0.2.0_20210721_153225/Windows/00check.log<https://win-builder.r-project.org/incoming_pretest/rtree_0.2.0_20210721_153225/Windows/00check.log> > cran-comments.md here: > https://github.com/akoyabio/rtree/blob/master/cran-comments.md<https://github.com/akoyabio/rtree/blob/master/cran-comments.md> > > Thank you for any guidance, > Kent Johnson > Akoya Biosciences > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel<https://stat.ethz.ch/mailman/listinfo/r-package-devel> > -- Michael http://www.dewey.myzen.co.uk/home.html<http://www.dewey.myzen.co.uk/home.html> [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] CRAN submission with warnings
Actually I think the contents of cran-comments.md were included in the comments on the submission form. I used devtools::submit_cran() for the submission. It automates the form submission and IIUC copies cran-comments into the form. My comments are in the confirmation email I received. Kent From: Kent Johnson Sent: Monday, July 26, 2021 1:38 PM To: Michael Dewey ; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] CRAN submission with warnings Thanks Michael! So I should re-submit the package with the documentation on WARNINGS in the comments section of the submission? Kent From: Michael Dewey Sent: Monday, July 26, 2021 12:07 PM To: Kent Johnson ; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] CRAN submission with warnings Dear Kent I think the canonical way to report these is in the space on the submission form, unless I have not correctly grasped what you did. Michael On 26/07/2021 16:02, Kent Johnson wrote: > Hi, > > What is the usual process to submit a new package to CRAN which has > false-positive warnings? > > I submitted rtree_0.2.0 last week (7/21). This package compiles with warnings > from Boost headers. The warnings are expected, unavoidable, and unimportant, > which I documented in cran-comments.md. After submitting the package, I got > an email that the package failed the pre-test due to the warnings. I > replied-all, pointing to the explanation in cran-comments.md. I haven't heard > anything since, and the package is still in the archive folder at > ftp://cran.r-project.org/incoming<ftp://cran.r-project.org/incoming>. > > I'm new to this process. Is there something else I should do, or should I > just sit tight and wait for a response? > > win-builder results are here: > https://win-builder.r-project.org/incoming_pretest/rtree_0.2.0_20210721_153225/Windows/00check.log<https://win-builder.r-project.org/incoming_pretest/rtree_0.2.0_20210721_153225/Windows/00check.log> > cran-comments.md here: > https://github.com/akoyabio/rtree/blob/master/cran-comments.md<https://github.com/akoyabio/rtree/blob/master/cran-comments.md> > > Thank you for any guidance, > Kent Johnson > Akoya Biosciences > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel<https://stat.ethz.ch/mailman/listinfo/r-package-devel> > -- Michael http://www.dewey.myzen.co.uk/home.html<http://www.dewey.myzen.co.uk/home.html> [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] CRAN submission with warnings
Thanks, Duncan, I did consult with Dirk about the warnings. The #pragma in Boost headers which disables those warnings is not allowed in a CRAN submission, so he removed the #pragma, enabling the warnings. I see that Boost does call std::abort in its error handling. I don't think I can do anything about that... Kent From: Duncan Murdoch Sent: Monday, July 26, 2021 3:12 PM To: Kent Johnson ; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] CRAN submission with warnings Regarding the issues: Since one of them comes from the BH package rather than yours, you might want to talk to Dirk for advice about it. The second issue you mention in your comment looks more serious: "Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C)". Your response that you don't call 'abort', 'exit' or 'printf' isn't sufficient here: those functions appear to have been linked in to your DLL, so somebody is calling them. I'd try to track down those calls and see if there's a way to compile without them. Duncan Murdoch > > win-builder results are here: > https://win-builder.r-project.org/incoming_pretest/rtree_0.2.0_20210721_153225/Windows/00check.log<https://win-builder.r-project.org/incoming_pretest/rtree_0.2.0_20210721_153225/Windows/00check.log> > cran-comments.md here: > https://github.com/akoyabio/rtree/blob/master/cran-comments.md<https://github.com/akoyabio/rtree/blob/master/cran-comments.md> > > Thank you for any guidance, > Kent Johnson > Akoya Biosciences > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel<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
Re: [R-pkg-devel] CRAN submission with warnings
The {anytime} package by Dirk Eddelbuettel uses {BH} and generates the same
NOTE when I CMD Check it locally on Windows. It seems safe to ignore this NOTE.
Kent
From: Duncan Murdoch
If you look at the BH page on CRAN, there are a ton of "reverse linking
to" packages, i.e. packages that are doing something like what you do.
It would be worth looking at a few of those that don't generate those
warnings (e.g. abcADM, ACEt, etc.) to see if they're using the same
parts of Boost as you're using, and have found a way to avoid the warnings.
Duncan Murdoch
>
> Kent
>
>
> *From:* Duncan Murdoch
> The second issue you mention in your comment looks more serious:
> "Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found
> 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf',
> possibly from 'printf' (C)".
>
> Your response that you don't call 'abort', 'exit' or 'printf' isn't
> sufficient here: those functions appear to have been linked in to your
> DLL, so somebody is calling them. I'd try to track down those calls and
> see if there's a way to compile without them.
>
> Duncan Murdoch
>
> >
> > win-builder results are here:
> https://win-builder.r-project.org/incoming_pretest/rtree_0.2.0_20210721_153225/Windows/00check.log<https://win-builder.r-project.org/incoming_pretest/rtree_0.2.0_20210721_153225/Windows/00check.log>
> <https://win-builder.r-project.org/incoming_pretest/rtree_0.2.0_20210721_153225/Windows/00check.log<https://win-builder.r-project.org/incoming_pretest/rtree_0.2.0_20210721_153225/Windows/00check.log>>
> > cran-comments.md here:
> https://github.com/akoyabio/rtree/blob/master/cran-comments.md<https://github.com/akoyabio/rtree/blob/master/cran-comments.md>
> <https://github.com/akoyabio/rtree/blob/master/cran-comments.md<https://github.com/akoyabio/rtree/blob/master/cran-comments.md>>
> >
> > Thank you for any guidance,
> > Kent Johnson
> > Akoya Biosciences
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel<https://stat.ethz.ch/mailman/listinfo/r-package-devel>
> <https://stat.ethz.ch/mailman/listinfo/r-package-devel<https://stat.ethz.ch/mailman/listinfo/r-package-devel>>
> >
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