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-boun...@r-project.org on behalf of sm...@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:
START QUOTE
* 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.
END QUOTE
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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