Hi, certainly these are good suggestions, but I would tend to simply add some whitelisting functionality if the cause is beyond the package's control.
In this case I doubt it is a handler for SIGABRT, since that would not go away with -O2, or would it ? For now, just adding -O2 on Linux would fix this issue. Yours, Steffen On Mi, 2017-04-12 at 10:07 -0400, Vincent Carey wrote: > > Suppose you had a handler for SIGABRT in your code. Could CMD check > check for that and, if found, refrain from warning? That is somewhat > involved and goes beyond Bioc but it seems a principled way of > dealing with operations in binary infrastructure whose behavior we > cannot control. The problem will surely arise in other settings. > Could BiocCheck prototype the approach? > > On Wed, Apr 12, 2017 at 9:12 AM, Kasper Daniel Hansen <kasperdanielha > n...@gmail.com> wrote: > > > > I think "we" have to appreciate that the warning about abort/etc > > and others > > is really hard to deal with when you're including (large) external > > source > > as you do in mzR and for example affxparser / Rgraphviz. Generally > > fixing > > those in external code requires a lot of effort, and the further > > effort to > > document that the included sources in the package are different > > from the > > official sources. I have had warnings about this in affxparser for > > a long, > > long time and no-one has bothered me over it. > > > > What might be nice is (somehow) setting a flag saying this should > > be > > ignored in the check process, but of course we don't want that flag > > to be > > set by the developer, because usually, these issues should be dealt > > with. > > So perhaps there is nothing to do and I always have to click on > > each build > > report to verify that there is only 1 warning from this issues and > > not > > others. > > > > Best, > > Kasper > > > > On Wed, Apr 12, 2017 at 7:22 AM, Neumann, Steffen <sneumann@ipb-hal > > le.de> > > wrote: > > > > > > > > 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-bio > > chemis > > > > > > 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-bio > > chemis > > > > > > 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 > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > -- 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