[Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'
Gordon K Smyth
@myth @end|ng |rom weh|@edu@@u
Sat Oct 17 00:59:40 CEST 2020
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
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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