Hi Martin and malbec2 admin(s): Some more digging revealed that malbec2 http://bioconductor.org/checkResults/devel/bioc-LATEST/malbec2-NodeInfo.html is using "CFLAGS=-g -O2 -Wall" but only "CXXFLAGS=-Wall" while e.g. tokay2 uses "CXXFLAGS=-O2 -Wall -mtune=core2"
The -O2 optimisation is getting rid of the abort() symbol, as shown in https://github.com/sneumann/xcms/issues/150#issuecomment-293545521 => Is there a way to get -O2 back on the BioC build machines ? This should fix our WARNING. Bonus: will fix the same issue in mzR :-) Yours, Steffen On So, 2017-04-02 at 10:01 -0400, Martin Morgan wrote: > > On 04/02/2017 06:52 AM, Neumann, Steffen wrote: > > > > [...] > > in preparation for the release, we are hunting down WARNINGS > > "Found ‘abort’, possibly from ‘abort’ (C)" in xcms/mzR. > > The abort() call is not coming from XCMS, but rather > > from the C++ code in the STL, and we have no idea [...] > > > > > We are tracking this in: > > https://github.com/sneumann/xcms/issues/150 [...] > > I don't think Bioconductor can help with this; maybe the Rcpp or R- > devel mailing lists? -- 3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017 http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-biochemis try-symposium/ -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 -- 3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017 http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-biochemis try-symposium/ -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel