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

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Mon Oct 19 19:40:44 CEST 2020

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 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:


    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

    Professor Gordon K Smyth
    Joint Head, Bioinformatics Division
    Walter and Eliza Hall Institute of Medical Research


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