[R-pkg-devel] CRAN submission with warnings

[Murray Efford]

FWIW my package 'secr' has for some time had the same 'abort', 'exit' or 'printf' issue when checked locally on Windows. It is happily accepted by CRAN, and I have learned to ignore the local message. The only common element I can see between secr 4.4.5 and rtree 0.2.0 is that both import and link to Rcpp.
Murray

________________________________________
From: R-package-devel <r-package-devel-bounces using r-project.org> on behalf of Duncan Murdoch <murdoch.duncan using gmail.com>
Sent: 27 July 2021 07:12
To: Kent Johnson; r-package-devel using r-project.org
Subject: Re: [R-pkg-devel] CRAN submission with warnings

On 26/07/2021 11:02 a.m., 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 https://apc01.safelinks.protection.outlook.com/?url=ftp%3A%2F%2Fcran.r-project.org%2Fincoming&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C06d4282ca217499e9a0508d950696dea%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637629236685044870%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=1FHh3TJIOfDVlt2AwP14VakVEnwmNhHNlNyMnbKZeFg%3D&reserved=0.
>
> I'm new to this process. Is there something else I should do, or should I just sit tight and wait for a response?

Generally I'd sit for a week or so, then send a gentle reminder.  It's
summer, and people are on holiday, so you might make that 10 days.

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://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwin-builder.r-project.org%2Fincoming_pretest%2Frtree_0.2.0_20210721_153225%2FWindows%2F00check.log&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C06d4282ca217499e9a0508d950696dea%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637629236685044870%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=So21y%2B0jedC7Sg77850LUBiVHqMzC2Dai9761M6MRwc%3D&reserved=0
> cran-comments.md here: https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fakoyabio%2Frtree%2Fblob%2Fmaster%2Fcran-comments.md&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C06d4282ca217499e9a0508d950696dea%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637629236685044870%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=JsNXbq4%2FNfAVQUJ1HrcbUyz%2FJBiOaMASZn9Q9c2jBnc%3D&reserved=0
>
> Thank you for any guidance,
> Kent Johnson
> Akoya Biosciences
>
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