[Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

Vincent Carey @tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Mon Oct 19 22:34:22 CEST 2020

On Mon, Oct 19, 2020 at 1:41 PM Martin Morgan <mtmorgan.bioc using gmail.com>

> Just to respond that I don't have a clear answer for you; I would guess
> that there is a change upstream of your package, and that the NOTE is
> spurious. If this also occurs on a non-Bioconductor Windows machine then it
> would be appropriate to bring this up on another forum, R-devel or
> R-package-devel (https://stat.ethz.ch/mailman/listinfo/r-package-devel),
> especially if the NOTE can be elicited by a trivial example package. I
> would assume that the NOTE is safe to ignore, but...

I was able to reproduce the abort notes using R 4.0.3 with current
rcmdcheck run over the limma_3.44.3.tar.gz on a non-bioconductor
windows machine.  I tried dependency walker on limma.dll there but did not
see any interesting data.  The notes occur with
IRanges on the machine I checked.

> I think the 'Dependency walker' utility could be used to investigate the
> DLL to identify where this comes from, but I don't have easy access to a
> Windows machine for this type of work.
> Martin Morgan
> On 10/16/20, 7:00 PM, "Bioc-devel on behalf of Gordon K Smyth" <
> bioc-devel-bounces using r-project.org on behalf of smyth using wehi.edu.au> wrote:
>     This is more an R question than a Bioconductor question, but I would
> be grateful if the Biocore team or other Bioc developers have any insight.
>     After upgrading to R 4.0.3 or R 4.1.0-devel, I find that running R CMD
> check under Windows now gives a worrying Note about .o files and 'abort'.
> The same warning occurs for all the packages I maintain that contain source
> code. The Note does not appear for R 4.0.2 or earlier.
>     An example of the Note is:
>     * checking compiled code ... NOTE
>     Note: information on .o files for x64 is not available
>     File
> 'c:/Gordon/software/gitbioc/limma.Rcheck/limma/libs/x64/limma.dll':
>       Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
>       Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
>       Found 'printf', possibly from 'printf' (C)
>     Compiled code should not call entry points which might terminate R nor
>     write to stdout/stderr instead of to the console, nor use Fortran I/O
>     nor system RNGs. The detected symbols are linked into the code but
>     might come from libraries and not actually be called.
>     I am baffled by the Note because my code does not contain any of the
> offending functions (abort, exit or printf) that the Note accuses me of.
> Surprisingly I can't find any recent chatter about this Note on the R-devel
> mailing list. There no mention of it in the Rtools documentation. I have
> also searched the R manual on Writing R Extensions but can't find anything
> that would cause a Windows-specific note.
>     I see from the build/check reports for Bioconductor 3.12 that I am not
> alone. The same Note appears in the Windows check logs for a very large
> number of Bioconductor packages, for example Biobase:
> http://bioconductor.org/checkResults/devel/bioc-LATEST/Biobase/riesling1-checksrc.html
>     I am guessing that the same Note now appears in the Windows check log
> for every Bioconductor package that contains any C or Fortran source code.
> The Note does not appear in the Linux or Mac check logs for the same
> packages.
>     My questions are:
>     1. Does anyone know what is causing this Note.
>     2. Can I fix the note? If not, can I ignore it?
>     I also wonder whether this Note will cause the CRAN maintainers to not
> accept my package submissions, but that is perhaps a question for another
> forum.
>     Thanks for any insights
>     Gordon
>     ------------------------------------------
>     Professor Gordon K Smyth
>     Joint Head, Bioinformatics Division
>     Walter and Eliza Hall Institute of Medical Research
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