On Mon, Oct 19, 2020 at 1:41 PM Martin Morgan <mtmorgan.b...@gmail.com> wrote:
> 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-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 > > _______________________________________________ > > The information in this email is confidential and intended solely for > the addressee. > You must not disclose, forward, print or use it without the permission > of the sender. > > The Walter and Eliza Hall Institute acknowledges the Wurundjeri people > of the Kulin > Nation as the traditional owners of the land where our campuses are > located and > the continuing connection to country and community. > _______________________________________________ > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
